Introduction to Biofilm Engineering

304 Pages·2020·43.896 MB·English

by  Navanietha Krishnaraj Rathinam (editor), Rajesh K. Sani (editor)

Introduction to Biofilm Engineering
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Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
1323
ACS SYMPOSIUM SERIES
Introduction to Biofilm Engineering
Navanietha Krishnaraj Rathinam,Editor
Department of Chemical and Biological Engineering
South Dakota School of Mines and Technology
Rapid City, South Dakota, United States
Rajesh K. Sani,Editor
Department of Chemical and Biological Engineering
Department of Applied Biological Sciences
South Dakota School of Mines and Technology
Rapid City, South Dakota, United States
American Chemical Society, Washington, DC
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
Library of Congress Cataloging-in-Publication Data
Names: Rathinam, Navanietha Krishnaraj, editor. | Sani, Rajesh K., editor.
Title: Introduction to biofilm engineering / Navanietha Krishnaraj
Rathinam, editor, Department of Chemical and Biological Engineering,
South Dakota School of Mines and Technology, Rapid City, South Dakota,
United States, Rajesh K. Sani, editor, Department of Chemical and
Biological Engineering, Department of Applied Biological Sciences, South
Dakota School of Mines and Technology, Rapid City, South Dakota, United
States.
Description: Washington, DC : American Chemical Society, [2019] | Series:
ACS symposium series; 1323 | Includes bibliographical references and
index.
Identifiers: LCCN 2019022979 (print) | LCCN 2019022980 (ebook) | ISBN
9780841234734 (hardcover) | ISBN 9780841234710 (ebook)
Subjects: LCSH: Biofilms. | Biofilms--Industrial applications. |
Bioremediation.
Classification: LCC QR100.8.B55 I58 2019 (print) | LCC QR100.8.B55
(ebook) | DDC 579/.17--dc23
LC record available at https://lccn.loc.gov/2019022979
LC ebook record available at https://lccn.loc.gov/2019022980
ThepaperusedinthispublicationmeetstheminimumrequirementsofAmericanNationalStandardforInformation
Sciences—Permanence of Paper for Printed Library Materials, ANSI Z39.48n1984.
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PRINTED IN THE UNITED STATES OF AMERICA
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
Foreword
Thepurposeoftheseriesistopublishtimely,comprehensivebooksdevelopedfromtheACS
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andcomprehensivecoverageandforinteresttotheaudience.Somepapersmaybeexcludedtobetter
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orintroductorychaptersareadded.Draftsofchaptersarepeer-reviewedpriortofinalacceptanceor
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Verbatim reproductions of previous published papers are not accepted.
ACS Books Department
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
Preface
Biofilms, ubiquitous in nature, have great potential as they possess inherent characteristics of
self-immobilization, high resistance to reactants, and long-term activity. Biofilms provide a stable
environmentforthemicroorganismsenclosedwithinthem,andtheirextracellularmatrixproffers
a higher resistance to extreme conditions of pH and temperature and to the presence of toxic
s.
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cl substances. Biofilms mediate several reactions in our day-to-day activities. Some examples of
d arti biofilm-mediated reactions include biofouling, biocorrosion of biomedical implants/scaffolds in
e
sh biologicalfluids,corrosionofmetalobjects(includingdecks,tanksofships,andoilpipelines),and
C).publi biocorrosion reactions in the deep biosphere and benthic zones.
UTare Biofilmshavebothpositiveandnegativeroles.Itisestimatedthatmorethan60%ofmicrobial
38 (y sh infections are caused by biofilms. Periodontitis, osteomyelitis, urinary tract infections, and dental
2:el
3:1mat caries are some examples. In addition, biofilms grow on the surfaces of medical devices such as
3, 2020 at 0ow to legiti ccadoatnvhateantctetargsle,esnpaseserswit,oenpll.eroaThslthdeeiratoliyclesiojsoficbnaittosh,fieltpmearscse,inmatnahkdeegrvsao,sitchreoeianprtrteossvttiahnlevaeslest,sr.accHteniostwrvaeiltvaelvref,onrtohhueusymcoaaffnthehereteatrrltesh,maeusnrtidnhoaeursyes
2h
h n biofilms produce several important compounds that offer immunity to the human body. Biofilms
Marcns o alsoplayakeyroleinimprovingthestabilityandcatalyticactivityofbioprocessesbecauseoftheir
73.50 on s for optio spyrsotdeumcattioicnoorfgainnidzuatsitorina.llyUsreeleovfanbtiocfiolmmspoiunnbdisop(erothcaenssoelsahnadvesuscecvienriaclaacdidva)nbtaygeasd,soforprtieoxna-mfipxeled,
ed via 155.69.1haringguideline bbdiieoosfiraelElimmnleaectrdtieoriaaonctai,tcooatnrinsv.deoreblweiocittfirhlom-cfseelrlmshaiemvnetmataoipobpnill.iizcBeaditoiofionlnmsaslignairneaptirenoddbiuespcatdeinsosnvasbolpeflafnobkriotboeinloeieccltaerlcilcytirtogyrcohawenmidnigcahclyedsllyrsso,tgeaemnnds,
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nloaorg/ as they mediate direct electron transfer. They have potential for improving efficiency and cutting
Dowbs.acs. dproewcinseclyosttasiloorfebditohprrooucgehssbeiso.fiThlmeesntgruinceteurrien,goarpgparnoizaacthioesn.,Thanids,ianrcthuirtnecwtuilrlefuorfthtehreebnihoafinlcmercaatnesboef
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s:// biocatalysistoimprovetheefficiencyofthebioprocesses.Owingtoadvancementsinthebiomedical
http sector, the market for biofilm control agents has improved tremendously in recent years.
ee Thereisagrowingdemandforinvestigationofbiofilmmechanismsindetailforthepurposeof
S
controllingdiseasesaswellasforharnessingtheirpotentialforindustrialbiotechnologyapplications.
Althoughbiofilmshavegreaterrolesindiseasebiologyandofferbetteryieldsthansuspendedcellsin
bioprocesses,littleemphasishasplacedonbiofilmsinseveraluniversities’curricula.Thisbookaims
to provide a basic understanding about biofilm formation, factors influencing biofilm formations,
andengineeringstrategiesforimprovingorinhibitingthegrowthofbiofilms.Thisbookwillserve
ascoursematerialfortheundergraduatestudents,graduatestudents,andfacultywhoareinterested
inofferingacourseonbiofilmengineering.Thisbookcoverstechniquesthatarerelevanttobiofilm
characterization, which will be helpful for the researchers to gain basic understanding about the
subject.
Biofilm engineering is highly interdisciplinary. Keeping this in mind, this book is designed
to cover both concepts of science and engineering in biofilms. This book covers the scientific
ix
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
background on factors that drive biofilm formation on surfaces including the genetic and
physiologicalcharacteristicsofthemicroorganismsaswellasthesurfacecharacteristicsthatinfluence
biofilmformation.Engineeringconceptsincludeanalyzingthebiofilmformation,advancedimaging
strategiesforunderstandingbiofilmarchitecture,mechanobiologyofbiofilms,geneticengineering
of microbes for improved biofilm formation and improved catalysis, mass transfer limitations in
biofilms, electron transfer mechanisms and kinetics in electroactive biofilms, biocorrosion in
implants and other structures in deep biosphere, modelling of biofilms, controlling biofilms, and
application of biofilms.
Theeditorsextendtheirheartfeltthankstoalltheauthorswhohavesignificantlycontributedto
thistextbook.Theeditorsalsoacknowledgethereviewersfortheirtimeinreviewingthechapters
extensively.TheeditorsalsothanktheeditorialofficeteamatACSwhohaveplayedacrucialrolein
the overall editing process.
Dr.Navanietha KrishnarajRathinam,Research Scientist-III
BuG ReMeDEE Consortium,
Department of Chemical and Biological Engineering,
South Dakota School of Mines and Technology,
501 E. St. Joseph Street
Rapid City, South Dakota 57701-3901
Dr.Rajesh K.Sani,Professor
BuG ReMeDEE Consortium,
Department of Chemical and Biological Engineering &
Chemistry and Applied Biological Sciences,
South Dakota School of Mines and Technology,
501 E. St. Joseph Street
Rapid City, South Dakota 57701-3901
x
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
Chapter1
Quorum Sensing inPseudomonas aeruginosaand Its
Relationship to Biofilm Development
JinshuiLin1,2,*andJuanliCheng1,2
s.
cle 1Shaanxi Engineering & Technological Research Center for Conservation & Utilization of
arti Regional Biological Resources, Yan’an University,
d
he Yan’an 716000, Shaanxi, People’s Republic of China
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Te Yan’an 716000, Shaanxi, People’s Republic of China
Uar
43 (y sh *E-mail:[email protected]@163.com.
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3, 2020 at 0ow to legiti PseudomonasaeruginosaisaGram-negative,rod-shapedbacteriumresponsiblefor
h 2n h severe and persistent infections in immunocompromised and cystic fibrosis
Marcns o patients. It is a highly recalcitrant pathogen because it is resistant to most
on ptio antimicrobialagents,makinginfectionsdifficulttotreatandcontain.Thisproblem
73.50 s for o isfurthercompoundedbytheabilityofP.aeruginosatoproduceabiofilmmatrix,
a 155.69.1gguideline wacgohemincmthsuinntcoicreatathisoeensabanantcditbeirgoieatnilcercereselilgssut.alanQtcoeuroybryuslymoswteemsreinntsghinathgtem(aQoccdSeu)sl,saitbeaislitbtyhacoetfeearxniaptlrimecsisecilrolo–nbceioalfll
ed viharin virulence and biofilm formation genes, is a potential target for developing new
ds
nloaorg/ therapiesagainstP.aeruginosainfection.Thischapterwillfocusonrecentadvances
Dows.acs. intargetingthefourmainQSsystems(las,rhl,pqs,andiqs)ofP.aeruginosaand
ub will specifically evaluate their role in biofilm development.
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1.Introduction
Pseudomonasaeruginosaisanopportunisticpathogenthatexistsinvariouseukaryotichosts,as
wellasinhost-freeenvironments(1).Theenvironmentalstrainsexpresstypicalvirulencefactorsand
multidrug resistance determinants, while the clinical strains can use oil hydrocarbons as a carbon
source.Therefore,environmentalandclinicalstrainsofP.aeruginosamaybefunctionallyequivalent
in several traits relevant for their virulence or environmental properties (1, 2). P. aeruginosa is
responsible for 10–20% of nosocomial infections (3) and has been ranked by the World Health
Organization as the priority-one human pathogen requiring development of novel antibacterial
agents(4–6).Itisacommoncauseofhospital-andcommunity-acquiredlung,skin,eye,wound,
bloodborne, and urinary tract infections (4, 7, 8) and is particularly hazardous for
© 2019 American Chemical Society
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
immunocompromised patients and those with cystic fibrosis (CF), burns, open fractures, or
implanted medical devices such as catheters (4, 9, 10). The pathogenicity of P. aeruginosa is
controlled by several virulence factors that aid tissue invasion and damage (2, 11). P. aeruginosa
hasanarmoryofcell-associated(flagella,pili,lectins,alginate/biofilm,andlipopolysaccharide)and
extracellular(proteases,hemolysins,cytotoxin,pyocyanin,siderophores,exotoxinA,exoenzymeS,
andexoenzymeU)virulencefactors(11,12).Theproductionofthesevirulencefactorsisinturn
dependentonquorumsensing(QS),theabilitytomonitorandrespondtochangesincellpopulation
density (11, 12). The QS systems of P. aeruginosa control several physiological aspects, such as
expressionofmultiplevirulencedeterminants,secondarymetaboliteproduction,swarmingmotility,
biofilm formation, biodegradation of pollutants, and electricity generation(13).
During chronic infections, P. aeruginosa forms biofilms, or adherent bacterial communities
surroundedbyanextracellularmatrixcomposedprimarilyofexopolysaccharides,proteins,lipids,
nucleicacids(extracellularDNAandRNA),andbiosurfactants(4,5,14).Biofilmformationinvolves
four main steps: attachment of the individual cells to a biotic or abiotic surface, multiplication,
microcolony formation, and maturation into a structured and resistant microbial community (5,
15).Biofilmsconferresistancetonotonlyantibioticsbutalsobacteriophages,disinfectants,andthe
hostimmunesystem,resultinginhighlyrecalcitrantinfections(5,16).SincebiofilmformationinP.
aeruginosaisregulatedbytheQSsystems,anydisruptioninthelattercanpotentiallypreventbiofilm
development(16),whichwouldnotonlydiminishtheriskofantibioticresistance,butalsoimprove
theresponseofmultidrug-resistant(MDR)strainstoantibiotics(17–19).Thischapterprovidesan
overviewoftheQSsystemsinbacteria,focusingmainlyonthosespecifictoP.aeruginosa,andtheir
role in biofilm formation.
2.Common Molecular Pathways Used by Bacteria for QS
Figure 1.Generalized model of a bacterial QS system.
2
Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.
QSisusedtodescribebacterialcommunicationandcollectiveresponsetocelldensitychanges
(20). It relies on the binding of small diffusible chemicals to cognate receptors, which trigger
expressionofgenesinvolvedincoordinatedactivities(Figure1)(20–23).ThebacterialQSsystems
are classified into three major types: (1) LuxI/LuxR-like that are present in many Gram-negative
speciesanduseacyl-homoserinelactones(AHL)asthesignalingmolecules,(2)oligopeptide-two-
componentpresentinmanyGram-positivespeciesthatusesmallpeptidesforsignaling,and(3)the
luxS-encodedautoinducer2(AI-2),whichispresentinseveralGram-negativeandGram-positive
species.RegardlessoftheQSsystem,anumberofstructurallydiversechemicalsareusedbybacteria
for cell-to-cell communication(20–24).
For LuxI/LuxR-like QS, the LuxI-like enzyme synthesizes specific AHLs from cellular
metabolites(20,25),likeS-adenosyl-L-methionineandspecificacyl–acylcarrierproteins(20,26).
TheAHLsdiffuseacrossthecellmembraneandaccumulateinproportiontothecelldensity.When
the population density reaches a certain threshold, the stored AHLs bind to the cognate LuxR-
likereceptors,andtheresultingcomplextranscriptionallyactivatestargetgenesbyinteractingwith
specific promoter sequences (20, 21, 25). All AHLs consist of a conserved homoserine lactone
ring, with the fatty acid side chains varying considerably in length, degree of saturation, and side
chain substitutions, depending on the specific QS system (20, 21, 25, 27). These differences are
responsible for the optimal binding between specific LuxR homologs to their respective cognate
AHL(22,27).Therefore,eachspeciesproducesauniqueAHLorauniquecombinationofAHLs
previously thought to only be recognized and responded to by members of the same species (21,
22,26).However,severalexamplesofcrosstalkbetweenAHLsignalingmicrobes,inwhichAHLs
producedbyonespeciescanbesensedbyotherspecies,havebeenreported(28).Particularly,AHLs
mediate communication betweenP. aeruginosaandBurkholderia cepaciain mixed biofilms(29).
Peptide-basedsignalingusuallyinvolvestheproductionofsmalllinearorcyclicpeptidesthatare
translatedasalargerprecursorandsubsequentlyprocessedbeforesecretion(21,25).Insomecases,
a membrane-bound sensor protein belonging to the two-component signal transduction family
interacts with the peptide, which then activates an associated response regulator that further
modulates expression of QS-regulated genes (20, 21, 25). In other cases, as with AHL-based
signaling, the peptide signal can also be internalized into the cytoplasm by a peptide-specific
transporter.Onceinternalized,thepeptidesignalinteractswithatranscriptionalregulator,inturn
activating downstream genes(21,30–32).
In addition to the aforementioned systems, the AI-2 QS has been detected in both Gram-
negative and Gram-positive bacteria (21, 22, 33). This has led to the hypothesis that AI-2 allows
interspeciescommunication,earningitthesobriquetof“bacterialEsperanto(20,21,33).”TheAI-
2 QS system was first described in Vibrio harveyi (34). The extracellular signaling molecule of the
V.harveyiAI-2systemisafuranosylboratediester(35),whichissynthesizedbytheluxSencoded
synthase(36).AnumberofstudieshaveshownthatAI-2signalingisresponsibleforspecificbacterial
phenotypes.However,mostofthesestudieshavereliedontheuseofluxSmutantstrains.AsLuxS
isinvolvedinrecyclingofS-adenosyl-L-methionine,thephenotypesobservedinthesemutantsmay
simplybeduetometabolicperturbations(20,37,38).Inthesecases,AI-2cannotbeconsidereda
signalingmoleculeateithertheintra-orinterspecieslevel(20).AlthoughluxShomologsarepresent
in many species, the signaling mechanism has not been completely defined or verified in most of
these systems(20).
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Rathinam and Sani; Introduction to Biofilm Engineering
ACS Symposium Series; American Chemical Society: Washington, DC, 2019.