Available online at www.sciencedirect.
com
Research in Microbiology 163 (2012) 695–702
1 Acinetobacter venetianus – Molecular and
16S, 18S – Megraft: a software package to
graft ribosomal small subunit (16S/18S)
fragments onto full-length sequences for
accurate species richness and sequencing
depth analysis in pyrosequencing-length
metagenomes and similar environmental
datasets, 407
16S rRNA – Biodiversity characterization of
cellulolytic bacteria present on native Chaco
soil by comparison of ribosomal RNA
genes, 221 – Shifts in phylogenetic diversity
of archaeal communities in mangrove
sediments at different sites and depths in
southeastern Brazil, 366 – Anaerobic
transformation of octahydro-1,3,5,7-
tetranitro-1,3,5,7-tetrazocine (HMX) by
ovine rumen microorganisms, 567
2 of Paracoccidioides brasiliensis during in
23S rRNA – Real-time PCR for Helicobacter
pylori quantification and detection
of clarithromycin resistance in gastric
tissue from patients with gastrointestinal
disorders, 109
3 adhesin biosynthesis, 674 – Atomic force
3D-SIM – Atomic force and super-resolution
microscopy support a role for LapA as a
cell-surface biofilm adhesin of Pseudomonas
fluorescens, 685
A pathogen adhesion to enterocytes in vitro, 22
abrB – Identification of the bacteriocin
subtilosin A and loss of purL results in its
high-level production in Bacillus
amyloliquefaciens, 470
Acetate metabolism – A positive selection
approach identifies residues important for
folding of Salmonella enterica Pat, an N-
lysine acetyltransferase that regulates
central metabolism enzymes, 427
Acetobacter aceti – Characterization of the
theta replication plasmid pGR7 from
Acetobacter aceti CCM 3610, 419
Acinetobacter calcoaceticus – Comparative
analysis of the complete genome of an
Acinetobacter calcoaceticus strain adapted
to a phenol-polluted environment, 36
Keyword index
phenotypic characterization of
Acinetobacter strains able to degrade diesel
fuel, 161
AckA – Elevated CpxR~P levels repress the
Ysc–Yop type III secretion system of
Yersinia pseudotuberculosis, 518
Acyl-homoserine lactone – Response of leaf-
associated bacterial communities to primary
acyl-homoserine lactone in the tobacco
phyllosphere, 119
Adherence – Which specificity in cooperation
between phytostimulating rhizobacteria and
plants?, 500 – Pili of Gram-positive bacteria:
roles in host colonization, 645
Adhesin – Comparative transcriptome analysis
vitro adhesion to type I collagen and
fibronectin: identification of potential
adhesins, 182 – New regulators of biofilm
development in Candida glabrata, 297 –
Phosphorus limitation increases attachment
in Agrobacterium tumefaciens and reveals a
conditional functional redundancy in
and super-resolution microscopy support a
role for LapA as a cell-surface biofilm
adhesin of Pseudomonas fluorescens, 685
Adhesion – Xylo-oligosaccharides inhibit
Aerobic spore-formers – Recognition of
greater diversity of Bacillus species and
related bacteria in human faeces, 3
Aeromonas – Novel gene cassettes and
integrons in antibiotic-resistant bacteria
isolated from urban wastewaters, 92
Aeromonas hydrophila – Recombinant
Aeromonas hydrophila outer membrane
protein 48 (Omp48) induces a protective
immune response against Aeromonas
hydrophila and Edwardsiella tarda, 286
Aeromonas spp. – First description of the
qnrS-like (qnrS5) gene and analysis of
quinolone resistance-determining regions in
motile Aeromonas spp. from diseased fish
and water, 73
http://www.elsevier.com/locate/resmic
AFLP – Characterization of atypical Listeria
innocua isolated from swine slaughterhouses
and meat markets, 268
AFM – Atomic force and super-resolution
microscopy support a role for LapA as a
cell-surface biofilm adhesin of Pseudomonas
fluorescens, 685
Alkaline phosphatase – Type II-dependent
secretion of a Pseudomonas aeruginosa
DING protein, 457
alkM gene – Molecular and phenotypic
characterization of Acinetobacter strains
able to degrade diesel fuel, 161
Alpha-Galactosidase – Aga1, the first alpha-
Galactosidase from the human bacteria
Ruminococcus gnavus E1, efficiently
transcribed in gut conditions, 14
Ammonium – Nitrate and ammonium uptake
by natural stream sediment microbial
communities in response to nutrient
enrichment, 137
Ammonium excretion – Involvement of the
ammonium transporter AmtB in nitrogenase
regulation and ammonium excretion in
Pseudomonas stutzeri A1501, 332
Ammonium transporter AmtB – Involvement
of the ammonium transporter AmtB in
nitrogenase regulation and ammonium
excretion in Pseudomonas stutzeri A1501,
332
Amyloid – Microbial manipulation of the
amyloid fold, 592
Antagonist – Streptomyces competition and
co-evolution in relation to plant disease
suppression, 490
Anti-virulence genes – Shedding of genes
that interfere with the pathogenic lifestyle:
the Shigella model, 399
Antibacterial activity – Identification of the
bacteriocin subtilosin A and loss of purL
results in its high-level production in
Bacillus amyloliquefaciens, 470
Antibiotics – Antibiotic and antimicrobial
peptide combinations: synergistic inhibition
of Pseudomonas fluorescens and antibiotic-
resistant variants, 101
696 Keyword index / Research in Microbiology 163 (2012) 695–702
Antibiotic resistance – Polyamines reduce
oxidative stress in Escherichia coli cells
exposed to bactericidal antibiotics, 83
Antifungal activity – Putative use of a
Bacillus subtilis L194 strain for biocontrol
of Phoma medicaginis in Medicago
truncatula seedlings, 388
Antimicrobial peptide – Synergistic effect of
antimicrobial peptide arenicin-1 in
combination with antibiotics against
pathogenic bacteria, 479
Antimicrobial resistance – Offense and
defense: microbial membrane vesicles play
both ways, 607
Aquaculture – Discovery of novel
biopreservation agents with inhibitory
effects on growth of food-borne pathogens
and their application to seafood products, 44
Archaea – Offense and defense: microbial
membrane vesicles play both ways, 607 –
Diversity, assembly and regulation of
archaeal type IV pili-like and non-type-IV
pili-like surface structures, 630
Archaellum – Diversity, assembly and
regulation of archaeal type IV pili-like and
non-type-IV pili-like surface structures, 630
Arenicin-1 – Synergistic effect of antimicrobial
peptide arenicin-1 in combination with
antibiotics against pathogenic bacteria, 479
Arenicola marina – Synergistic effect of
antimicrobial peptide arenicin-1 in
combination with antibiotics against
pathogenic bacteria, 479
ARS silencing – Structure, replication
efficiency and fragility of yeast ARS
elements, 243
Atomic force microscopy – Antibacterial
activity of class IIa bacteriocin Cbn BM1
depends on the physiological state of the
target bacteria, 323
Autonomously replicating sequences –
Structure, replication efficiency and fragility
of yeast ARS elements, 243
B bacteriocin Cbn BM1 depends on the
b-lactamase – Cefoxitin is both an inhibitor
of class A beta-lactamase of Xanthomonas
campestris pv. campestris str. 17 and an
inducer of its gene, 550
Bacillus – Recognition of greater diversity of
Bacillus species and related bacteria in
human faeces, 3
Bacillus amyloliquefaciens – Identification of
the bacteriocin subtilosin A and loss of purL
results in its high-level production in
Bacillus amyloliquefaciens, 470
Bacillus subtilis – Putative use of a Bacillus
subtilis L194 strain for biocontrol of Phoma
medicaginis in Medicago truncatula
seedlings, 388
Bacterial community – Response of leaf-
associated bacterial communities to primary
acyl-homoserine lactone in the tobacco
phyllosphere, 119 – Fate of invading
bacteria in soil and survival of transformants
after simulated uptake of transgenes, as
evaluated by a model system based on
lindane degradation, 200
Bacterial community structure – Influence
of nitrogen fertilization on diazotrophic
communities in the rhizosphere of the
Jerusalem artichoke (Helianthus tuberosus
L.), 349
Bacterial diversity – Impact of salinity-
tolerant MCM6 transgenic tobacco on soil
enzymatic activities and the functional
diversity of rhizosphere microbial
communities, 511
Bacterial genome – Shedding of genes that
interfere with the pathogenic lifestyle: the
Shigella model, 399
Bacterial load – Real-time PCR for
Helicobacter pylori quantification and
detection of clarithromycin resistance in
gastric tissue from patients with
gastrointestinal disorders, 109
Bacterial membrane – Synergistic effect of
antimicrobial peptide arenicin-1 in
combination with antibiotics against
pathogenic bacteria, 479
Bacterial motility – Physics of bacterial near-
surface motility using flagella and type IV
pili: implications for biofilm formation, 619
Bacterial pathogenesis – Offense and
defense: microbial membrane vesicles play
both ways, 607
Bacteriocins – Discovery of novel
biopreservation agents with inhibitory
effects on growth of food-borne pathogens
and their application to seafood products, 44
Bacteriocin – Antibacterial activity of class IIa
physiological state of the target bacteria, 323
Bacteriophage – Characterization of
endolysin from a Salmonella Typhimurium-
infecting bacteriophage SPN1S, 233
Biglycan – Real-time monitoring of the
adherence of Streptococcus anginosus
group bacteria to extracellular matrix
decorin and biglycan proteoglycans in
biofilm formation, 436
Biocontrol – Putative use of a Bacillus subtilis
L194 strain for biocontrol of Phoma
medicaginis in Medicago truncatula
seedlings, 388 – Streptomyces competition
and co-evolution in relation to plant disease
suppression, 490
Biodiversity – Biogeographical diversity of
leaf-associated microbial communities from
salt-secreting Tamarix trees of the Dead Sea
region, 142 – Biodiversity characterization
of cellulolytic bacteria present on native
Chaco soil by comparison of ribosomal
RNA genes, 221
Biofilm – Deletion of penicillin-binding
protein 1b impairs biofilm formation and
motility in Escherichia coli, 254 – Effects
of non-ionic solute stresses on biofilm
formation and lipopolysaccharide
production in Escherichia coli O157:H7,
258 – New regulators of biofilm
development in Candida glabrata, 297 –
Biochemical and genetic characteristics
of Cronobacter sakazakii biofilm
formation, 448 – Biofilm generation by
Piscirickettsia salmonis under growth
stress conditions: a putative in vivo
survival/persistence strategy in marine
environments, 557 – Microbial
manipulation of the amyloid fold, 592 –
Offense and defense: microbial membrane
vesicles play both ways, 607 – Pili of
Gram-positive bacteria: roles in host
colonization, 645 – Phosphorus limitation
increases attachment in Agrobacterium
tumefaciens and reveals a conditional
functional redundancy in adhesin
biosynthesis, 674 – Atomic force and
super-resolution microscopy support a
role for LapA as a cell-surface biofilm
adhesin of Pseudomonas fluorescens, 685
Biofilm formation – Physics of bacterial near-
surface motility using flagella and type IV
pili: implications for biofilm formation, 619
Biogeography – Biogeographical diversity of
leaf-associated microbial communities from
salt-secreting Tamarix trees of the Dead Sea
region, 142
blaxccgene ampR gene – Cefoxitin is both an
inhibitor of class A beta-lactamase of
Xanthomonas campestris pv. campestris str.
17 and an inducer of its gene, 550
C
Campylobacter jejuni – Reverse transcriptase
real-time PCR for detection and quantification
of viable Campylobacter jejuni directly from
poultry faecal samples, 64
Candida glabrata – New regulators of biofilm
development in Candida glabrata, 297
Carnobacterium – Antibacterial activity of class
IIa bacteriocin Cbn BM1 depends on the
physiological state of the target bacteria, 323
Cefoxitin – Cefoxitin is both an inhibitor of
class A beta-lactamase of Xanthomonas
campestris pv. campestris str. 17 and an
inducer of its gene, 550
Cell aggregation – Biofilm generation by
Piscirickettsia salmonis under growth
stress conditions: a putative in vivo
survival/persistence strategy in marine
environments, 557
 Keyword index / Research in Microbiology 163 (2012) 695–702 697
Cell–cell signaling – Myxobacterial tools for
social interactions, 579
Cellular immunity – Attenuated Listeria
monocytogenes, a Mycobacterium
tuberculosis ESAT-6 antigen expression and
delivery vector for inducing an immune
response, 540
Cellulose – Biodiversity characterization of
cellulolytic bacteria present on native Chaco
soil by comparison of ribosomal RNA
genes, 221
Cerebrospinal fluid – Enhanced activity of
linezolid against Staphylococcus aureus in
cerebrospinal fluid, 157
Chemotaxis – Which specificity in cooperation
between phytostimulating rhizobacteria and
plants?, 500
Chondroitin 4-sulphate – Real-time
monitoring of the adherence of Streptococcus
anginosus group bacteria to extracellular
matrix decorin and biglycan proteoglycans
in biofilm formation, 436
Chromatin – New regulators of biofilm
development in Candida glabrata, 297
CLPP – Impact of salinity-tolerant MCM6
transgenic tobacco on soil enzymatic
activities and the functional diversity of
rhizosphere microbial communities, 511
Colistin – Antibiotic and antimicrobial peptide
combinations: synergistic inhibition of
Pseudomonas fluorescens and antibiotic-
resistant variants, 101
Comparative genomics – Comparative
analysis of the complete genome of an
Acinetobacter calcoaceticus strain adapted
to a phenol-polluted environment, 36
Cooper transporter – Comparative
transcriptome analysis of Paracoccidioides
brasiliensis during in vitro adhesion to type
I collagen and fibronectin: identification of
potential adhesins, 182
Cooperation – Which specificity in
cooperation between phytostimulating
rhizobacteria and plants?, 500
Copper – Adaptation of Rhodococcus
erythropolis cells for growth and
bioremediation under extreme conditions,
125
CpxA – Elevated CpxR~P levels repress the
Ysc–Yop type III secretion system of
Yersinia pseudotuberculosis, 518
Crenarchaeota – Shifts in phylogenetic
diversity of archaeal communities in
mangrove sediments at different sites and
depths in southeastern Brazil, 366
Cronobacter sakazakii – Biochemical and
genetic characteristics of Cronobacter
sakazakii biofilm formation, 448
Crop – Differences in crop bacterial
community structure between hoatzins from
different geographical locations, 211
Cryptic plasmid – Characterization of the
theta replication plasmid pGR7 from
Acetobacter aceti CCM 3610, 419
Cytotoxicity – Screening of nuclear targeting
proteins in Acinetobacter baumannii based
on nuclear localization signals, 279
D
Decorin – Real-time monitoring of the
adherence of Streptococcus anginosus
group bacteria to extracellular matrix
decorin and biglycan proteoglycans in
biofilm formation, 436
Denaturing gradient gel electrophoresis
(DGGE) – Microbial community structure
stability, a key parameter in monitoring the
development of constructed wetland
mesocosms during start-up, 28,
Biogeographical diversity of leaf-associated
microbial communities from salt-secreting
Tamarix trees of the Dead Sea region, 142
Dermatan sulphate – Real-time monitoring
of the adherence of Streptococcus anginosus
group bacteria to extracellular matrix
decorin and biglycan proteoglycans in
biofilm formation, 436
Diazotrophs – Influence of nitrogen
fertilization on diazotrophic communities in
the rhizosphere of the Jerusalem artichoke
(Helianthus tuberosus L.), 349
Diet – Differences in crop bacterial community
structure between hoatzins from different
geographical locations, 211
Dimorphism – Identification of dimorphism-
involved genes of Yarrowia lipolytica by
means of microarray analysis, 378
Dimorphism-involved genes – Identification
of dimorphism-involved genes of Yarrowia
lipolytica by means of microarray analysis,
378
DING protein – Type II-dependent secretion
of a Pseudomonas aeruginosa DING
protein, 457
DNA damage – Polyamines reduce oxidative
stress in Escherichia coli cells exposed to
bactericidal antibiotics, 83
E
Edwardsiella tarda – Recombinant Aeromonas
hydrophila outer membrane protein 48
(Omp48) induces a protective immune
response against Aeromonas hydrophila and
Edwardsiella tarda, 286
Endolysin – Characterization of endolysin
from a Salmonella Typhimurium-infecting
bacteriophage SPN1S, 233
Enolase – Comparative transcriptome analysis
of Paracoccidioides brasiliensis during in
vitro adhesion to type I collagen and
fibronectin: identification of potential
adhesins, 182
Enterobacteriaceae – Novel gene cassettes
and integrons in antibiotic-resistant bacteria
isolated from urban wastewaters, 92
Enterococcus – Discovery of novel
biopreservation agents with inhibitory
effects on growth of food-borne pathogens
and their application to seafood products, 44
Envelope stress response – Offense and
defense: microbial membrane vesicles play
both ways, 607
Epiphytes – Response of leaf-associated
bacterial communities to primary acyl-
homoserine lactone in the tobacco
phyllosphere, 119
ESAT-6 antigen – Attenuated Listeria
monocytogenes, a Mycobacterium
tuberculosis ESAT-6 antigen expression and
delivery vector for inducing an immune
response, 540
Escherichia coli – Deletion of penicillin-
binding protein 1b impairs biofilm formation
and motility in Escherichia coli, 254 –
Variability of the tandem repeat region of
the Escherichia coli tolA gene, 316
Escherichia coli O157 – Effects of non-ionic
solute stresses on biofilm formation and
lipopolysaccharide production in
Escherichia coli O157:H7, 258
Euryarchaeota – Shifts in phylogenetic
diversity of archaeal communities in
mangrove sediments at different sites and
depths in southeastern Brazil, 366
Evolution – Shedding of genes that interfere
with the pathogenic lifestyle: the Shigella
model, 399
Exopolysaccharide – Biofilm generation by
Piscirickettsia salmonis under growth stress
conditions: a putative in vivo survival/
persistence strategy in marine environments,
557
Extracellular matrix – Microbial
manipulation of the amyloid fold, 592
Extracellular polymeric substances (EPS)
– Diversity of tailed phages in Baltic Sea
sediment: large number of siphoviruses with
extremely long tails, 292
Extreme conditions – Adaptation of
Rhodococcus erythropolis cells for growth
and bioremediation under extreme
conditions, 125
F
Fermented milk – Comparative analysis of
the gene expression profile of probiotic
Lactobacillus casei Zhang with and without
fermented milk as a vehicle during transit in
a simulated gastrointestinal tract, 357
Fiber – Microbial manipulation of the amyloid
fold, 592
698 Keyword index / Research in Microbiology 163 (2012) 695–702
Fish – Discovery of novel biopreservation
agents with inhibitory effects on growth of
food-borne pathogens and their application
to seafood products, 44
Flagella – Physics of bacterial near-surface
motility using flagella and type IV pili:
implications for biofilm formation, 619
Flp pilus – Neglected but amazingly diverse
type IVb pili, 659
Food-borne pathogens – Discovery of novel
biopreservation agents with inhibitory
effects on growth of food-borne pathogens
and their application to seafood products, 44
Fragile sites – Structure, replication efficiency
and fragility of yeast ARS elements, 243
Fruiting body – Myxobacterial tools for
social interactions, 579
FtsH metalloprotease – The sporulation
control gene spo0M of Bacillus subtilis is a
target of the FtsH metalloprotease, 114
G hrpL – Carbon source and cell density-
Gastrointestinal tract – Comparative analysis
of the gene expression profile of probiotic
Lactobacillus casei Zhang with and without
fermented milk as a vehicle during transit in
a simulated gastrointestinal tract, 357
Gateway cloning system – Screening of
nuclear targeting proteins in Acinetobacter
baumannii based on nuclear localization
signals, 279
Gene expression – Comparative analysis of
the gene expression profile of probiotic
Lactobacillus casei Zhang with and without
fermented milk as a vehicle during transit in
a simulated gastrointestinal tract, 357 –
Identification of dimorphism-involved
genes of Yarrowia lipolytica by means of
microarray analysis, 378
Genome evolution – Type II-dependent
secretion of a Pseudomonas aeruginosa
DING protein, 457
Genomics – Type II-dependent secretion of a
Pseudomonas aeruginosa DING protein, 457
Gram-positive bacteria – Pili of Gram-
positive bacteria: roles in host colonization,
645
Green manure – Streptomyces competition
and co-evolution in relation to plant disease
suppression, 490
Gut microbiota – Recognition of greater
diversity of Bacillus species and related
bacteria in human faeces, 3 – Aga1, the first
alpha-Galactosidase from the human
bacteria Ruminococcus gnavus E1,
efficiently transcribed in gut conditions, 14
H lindane degradation, 200
Helicase activity – Characterization of the
theta replication plasmid pGR7 from
Acetobacter aceti CCM 3610, 419
Helicobacter pylori – Real-time PCR for
Helicobacter pylori quantification and
detection of clarithromycin resistance in
gastric tissue from patients with
gastrointestinal disorders, 109
Heterogeneity – Pili of Gram-positive
bacteria: roles in host colonization, 645
Hfq-dependent stability – Two sRNA RyhB
homologs from Yersinia pestis biovar
microtus expressed in vivo have differential
Hfq-dependent stability, 413
Histidine kinase – Characterization of
sporulation histidine kinases of
Paenibacillus polymyxa, 272
HMX – Anaerobic transformation of
octahydro-1,3,5,7-tetranitro-1,3,5,7-
tetrazocine (HMX) by ovine rumen
microorganisms, 567
Host specificity – Which specificity in
cooperation between phytostimulating
rhizobacteria and plants?, 500
dependent regulation of type III secretion
system gene expression in Pseudomonas
syringae pathovar tomato DC3000, 531
hrpR – Carbon source and cell density-
dependent regulation of type III secretion
system gene expression in Pseudomonas
syringae pathovar tomato DC3000, 531
hrpS – Carbon source and cell density-
dependent regulation of type III secretion
system gene expression in Pseudomonas
syringae pathovar tomato DC3000, 531
Hydraulic conductivity – Microbial
community structure stability, a key
parameter in monitoring the development of
constructed wetland mesocosms during
start-up, 28
Hydroxyl radical – Synergistic effect of
antimicrobial peptide arenicin-1 in
combination with antibiotics against
pathogenic bacteria, 479
I
Immune response – Recombinant Aeromonas
hydrophila outer membrane protein 48
(Omp48) induces a protective immune
response against Aeromonas hydrophila and
Edwardsiella tarda, 286
In vivo expression – Aga1, the first alpha-
Galactosidase from the human bacteria
Ruminococcus gnavus E1, efficiently
transcribed in gut conditions, 14
Indigenous bacteria – Fate of invading
bacteria in soil and survival of transformants
after simulated uptake of transgenes, as
evaluated by a model system based on
Indole – Deletion of penicillin-binding protein
1b impairs biofilm formation and motility in
Escherichia coli, 254
Inoculation – Streptomyces competition and
co-evolution in relation to plant disease
suppression, 490
Integrons – Novel gene cassettes and integrons
in antibiotic-resistant bacteria isolated from
urban wastewaters, 92
Interaction – Response of leaf-associated
bacterial communities to primary acyl-
homoserine lactone in the tobacco
phyllosphere, 119
J
Jerusalem artichoke – Influence of nitrogen
fertilization on diazotrophic communities in
the rhizosphere of the Jerusalem artichoke
(Helianthus tuberosus L.), 349
L
Labeo rohita – Recombinant Aeromonas
hydrophila outer membrane protein 48
(Omp48) induces a protective immune
response against Aeromonas hydrophila and
Edwardsiella tarda, 286
Lactobacillus casei Zhang – Comparative
analysis of the gene expression profile of
probiotic Lactobacillus casei Zhang with
and without fermented milk as a vehicle
during transit in a simulated gastrointestinal
tract, 357
LC–MS/MS – Anaerobic transformation of
octahydro-1,3,5,7-tetranitro-1,3,5,7-
tetrazocine (HMX) by ovine rumen
microorganisms, 567
Lectins – Biofilm generation by Piscirickettsia
salmonis under growth stress conditions: a
putative in vivo survival/persistence strategy
in marine environments, 557
LH-PCR – Influence of nitrogen fertilization
on diazotrophic communities in the
rhizosphere of the Jerusalem artichoke
(Helianthus tuberosus L.), 349
Lindane – Fate of invading bacteria in soil and
survival of transformants after simulated
uptake of transgenes, as evaluated by a model
system based on lindane degradation, 200
Linezolid – Enhanced activity of linezolid
against Staphylococcus aureus in
cerebrospinal fluid, 157
Lipopeptides – Putative use of a Bacillus
subtilis L194 strain for biocontrol of Phoma
medicaginis in Medicago truncatula
seedlings, 388
Lipopolysaccharide – Effects of non-ionic
solute stresses on biofilm formation and
lipopolysaccharide production in
Escherichia coli O157:H7, 258
Listeria innocua – Characterization of
atypical Listeria innocua isolated from
swine slaughterhouses and meat markets,
268
 Keyword index / Research in Microbiology 163 (2012) 695–702 699
Listeria monocytogenes – Xylo-
oligosaccharides inhibit pathogen adhesion
to enterocytes in vitro, 22 – Characterization
of atypical Listeria innocua isolated from
swine slaughterhouses and meat markets,
268 – Attenuated Listeria monocytogenes, a
Mycobacterium tuberculosis ESAT-6
antigen expression and delivery vector for
inducing an immune response, 540
Lysine acylation – A positive selection
approach identifies residues important for
folding of Salmonella enterica Pat, an N-
lysine acetyltransferase that regulates
central metabolism enzymes, 427
M and quorum quenching, 173
Marine sediment – Diversity of tailed phages
in Baltic Sea sediment: large number of
siphoviruses with extremely long tails, 292
Mechanism of action – Antibacterial activity
of class IIa bacteriocin Cbn BM1 depends
on the physiological state of the target
bacteria, 323
Medicago truncatula – Putative use of a
Bacillus subtilis L194 strain for biocontrol
of Phoma medicaginis in Medicago
truncatula seedlings, 388
Membrane fusion – Myxobacterial tools for
social interactions, 579
Membrane rigidity – Effects of non-ionic
solute stresses on biofilm formation and
lipopolysaccharide production in
Escherichia coli O157:H7, 258
Meningococcus – A cell-contact-regulated
operon is involved in genetic variability in
Neisseria meningitidis, 192
Mesophile – Adaptation of Rhodococcus
erythropolis cells for growth and
bioremediation under extreme conditions, 125
Metabolic regulation – A positive selection
approach identifies residues important for
folding of Salmonella enterica Pat, an N-
lysine acetyltransferase that regulates
central metabolism enzymes, 427
Metabolites – Complexity of cell–cell
interactions between Pseudomonas sp. AS1
and Acinetobacter oleivorans DR1:
metabolic commensalism, biofilm formation
and quorum quenching, 173
Metagenomics – Megraft: a software package
to graft ribosomal small subunit (16S/18S)
fragments onto full-length sequences for
accurate species richness and sequencing
depth analysis in pyrosequencing-length
metagenomes and similar environmental
datasets, 407
Microarray analysis – Identification of
dimorphism-involved genes of Yarrowia
lipolytica by means of microarray analysis,
378
Microbial community structure – Microbial
community structure stability, a key
parameter in monitoring the development of
constructed wetland mesocosms during
start-up, 28
Microbial ecology – Recognition of greater
diversity of Bacillus species and related
bacteria in human faeces, 3
Microbiota – Differences in crop bacterial
community structure between hoatzins from
different geographical locations, 211
Mixed culture – Complexity of cell–cell
interactions between Pseudomonas sp. AS1
and Acinetobacter oleivorans DR1:
metabolic commensalism, biofilm formation
Mobile genetic elements – Novel gene
cassettes and integrons in antibiotic-
resistant bacteria isolated from urban
wastewaters, 92
mRNA fingerprints – Aga1, the first alpha-
Galactosidase from the human bacteria
Ruminococcus gnavus E1, efficiently
transcribed in gut conditions, 14
mRNA – Reverse transcriptase real-time PCR
for detection and quantification of viable
Campylobacter jejuni directly from poultry
faecal samples, 64
Multiresistance – Novel gene cassettes and
integrons in antibiotic-resistant bacteria
isolated from urban wastewaters, 92
Mutant – Mutational analysis of Pseudomonas
aeruginosa OxyR to define the regions
required for peroxide resistance and acute
virulence, 55
Mutation – A cell-contact-regulated operon is
involved in genetic variability in Neisseria
meningitidis, 192
Membrane vesicles – Offense and defense:
microbial membrane vesicles play both
ways, 607
Mycobacterium tuberculosis – Attenuated
Listeria monocytogenes, a Mycobacterium
tuberculosis ESAT-6 antigen expression and
delivery vector for inducing an immune
response, 540
N defense: microbial membrane vesicles play
Naphthalene – Complexity of cell–cell
interactions between Pseudomonas sp. AS1
and Acinetobacter oleivorans DR1:
metabolic commensalism, biofilm formation
and quorum quenching, 173
Native forest soil – Biodiversity
characterization of cellulolytic bacteria
present on native Chaco soil by comparison
of ribosomal RNA genes, 221
Nisin Z – Antibiotic and antimicrobial peptide
combinations: synergistic inhibition of
Pseudomonas fluorescens and antibiotic-
resistant variants, 101
Nitrate – Nitrate and ammonium uptake by
natural stream sediment microbial
communities in response to nutrient
enrichment, 137
Nitrate assimilation – Terminal reduction
reactions of nitrate and sulfate assimilation
in Streptomyces coelicolor A3(2):
identification of genes encoding nitrite and
sulfite reductases, 340
Nitrite reduction – Terminal reduction
reactions of nitrate and sulfate assimilation
in Streptomyces coelicolor A3(2):
identification of genes encoding nitrite and
sulfite reductases, 340
Nitrogen – Nitrate and ammonium uptake by
natural stream sediment microbial
communities in response to nutrient
enrichment, 137
Nitrogenase regulation – Involvement of the
ammonium transporter AmtB in nitrogenase
regulation and ammonium excretion in
Pseudomonas stutzeri A1501, 332
Non-ionic solute stress – Effects of non-ionic
solute stresses on biofilm formation and
lipopolysaccharide production in
Escherichia coli O157:H7, 258
Nuclear export signal – Screening of nuclear
targeting proteins in Acinetobacter
baumannii based on nuclear localization
signals, 279
Nuclear targeting proteins – Screening of
nuclear targeting proteins in Acinetobacter
baumannii based on nuclear localization
signals, 279
Nutrient loading – Nitrate and ammonium
uptake by natural stream sediment microbial
communities in response to nutrient
enrichment, 137
O
Omp48 – Recombinant Aeromonas hydrophila
outer membrane protein 48 (Omp48)
induces a protective immune response
against Aeromonas hydrophila and
Edwardsiella tarda, 286
Outer membrane vesicles – Offense and
both ways, 607
Operon – A cell-contact-regulated operon is
involved in genetic variability in Neisseria
meningitidis, 192
Organic amendment – Streptomyces
competition and co-evolution in relation to
plant disease suppression, 490
Outer membrane protein – Recombinant
Aeromonas hydrophila outer membrane
protein 48 (Omp48) induces a protective
immune response against Aeromonas
hydrophila and Edwardsiella tarda, 286
700 Keyword index / Research in Microbiology 163 (2012) 695–702

OxyR – Mutational analysis of Pseudomonas
aeruginosa OxyR to define the regions
required for peroxide resistance and acute
virulence, 55
P
Paenibacillus polymyxa – Characterization of
sporulation histidine kinases of
Paenibacillus polymyxa, 272
Paracoccidioides brasiliensis – Comparative
transcriptome analysis of Paracoccidioides
brasiliensis during in vitro adhesion to type
I collagen and fibronectin: identification of
potential adhesins, 182
Phosphate-binding protein – Type
II-dependent secretion of a Pseudomonas
aeruginosa DING protein, 457
Phosphorelay – Characterization
sporulation histidine kinases
Paenibacillus polymyxa, 272
Phyllosphere – Response of leaf-associated
bacterial communities to primary acyl-
homoserine lactone in the tobacco
phyllosphere, 119
Phylogenetics – Anaerobic transformation of
octahydro-1,3,5,7-tetranitro-1,3,5,7-
tetrazocine (HMX) by ovine rumen
microorganisms, 567
Protein acetyltransferases – A positive
selection approach identifies residues
important for folding of Salmonella enterica
Pat, an N-lysine acetyltransferase that
of regulates central metabolism enzymes, 427
of
Protein secretion – Type II-dependent
secretion of a Pseudomonas aeruginosa
DING protein, 457
Protein transfer – Myxobacterial tools for
social interactions, 579
Proteomics – The sporulation control gene
spo0M of Bacillus subtilis is a target of the
FtsH metalloprotease, 114

Pathoadaptive mutations – Shedding of
genes that interfere with the pathogenic
lifestyle: the Shigella model, 399
Pea MCM – Impact of salinity-tolerant
MCM6 transgenic tobacco on soil enzymatic
activities and the functional diversity of
rhizosphere microbial communities, 511
Pediocin PA-1/AcH – Antibiotic and
antimicrobial peptide combinations:
synergistic inhibition of Pseudomonas
fluorescens and antibiotic-resistant variants,
101
Penicillin-binding protein 1b – Deletion of
penicillin-binding protein 1b impairs
biofilm formation and motility in
Escherichia coli, 254
Peptidoglycan hydrolase – Characterization
of endolysin from a Salmonella
Typhimurium-infecting bacteriophage
SPN1S, 233
Peroxide resistance – Mutational analysis of
Pseudomonas aeruginosa OxyR to define
the regions required for peroxide resistance
and acute virulence, 55
Phage morphology – Diversity of tailed phages
in Baltic Sea sediment: large number of
siphoviruses with extremely long tails, 292
Phenol degradation – Comparative analysis
of the complete genome of an Acinetobacter
calcoaceticus strain adapted to a phenol-
polluted environment, 36
Phenotype microarray – Molecular and
phenotypic characterization of
Acinetobacter strains able to degrade diesel
fuel, 161
Phoma medicaginis – Putative use of a
Bacillus subtilis L194 strain for biocontrol
of Phoma medicaginis in Medicago
truncatula seedlings, 388
PhoR–PhoB – Phosphorus limitation
increases attachment in Agrobacterium
tumefaciens and reveals a conditional
functional redundancy in adhesin
biosynthesis, 674
Phosphate limitation – Phosphorus limitation
increases attachment in Agrobacterium
tumefaciens and reveals a conditional
functional redundancy in adhesin
biosynthesis, 674
Piscirickettsia salmonis – Biofilm generation
by Piscirickettsia salmonis under growth
stress conditions: a putative in vivo survival/
persistence strategy in marine environments,
557
Pilus – Pili of Gram-positive bacteria: roles in
host colonization, 645
Plant genotype – Which specificity in
cooperation between phytostimulating
rhizobacteria and plants?, 500
Plant growth-promoting rhizobacteria –
Which specificity in cooperation between
phytostimulating rhizobacteria and plants?,
500
Plasmid-mediated quinolone resistance –
First description of the qnrS-like (qnrS5)
gene and analysis of quinolone resistance-
determining regions in motile Aeromonas
spp. from diseased fish and water, 73
Point mutations – Real-time PCR for
Helicobacter pylori quantification and
detection of clarithromycin resistance in
gastric tissue from patients with
gastrointestinal disorders, 109
Polyamines – Polyamines reduce oxidative
stress in Escherichia coli cells exposed to
bactericidal antibiotics, 83 – Shedding of
genes that interfere with the pathogenic
lifestyle: the Shigella model, 399
Populations – Differences in crop bacterial
community structure between hoatzins from
different geographical locations, 211
Post-translational modification – A positive
selection approach identifies residues
important for folding of Salmonella enterica
Pat, an N-lysine acetyltransferase that
regulates central metabolism enzymes, 427
Prebiotics – Xylo-oligosaccharides inhibit
pathogen adhesion to enterocytes in vitro, 22
Probiotics – Discovery of novel
biopreservation agents with inhibitory
effects on growth of food-borne pathogens
and their application to seafood products, 44
Protein acetylation – A positive selection
approach identifies residues important for
folding of Salmonella enterica Pat, an N-
lysine acetyltransferase that regulates
central metabolism enzymes, 427
Pseudomonas aeruginosa – Mutational
analysis of Pseudomonas aeruginosa OxyR
to define the regions required for peroxide
resistance and acute virulence, 55
Pseudomonas fluorescens – Antibiotic and
antimicrobial peptide combinations:
synergistic inhibition of Pseudomonas
fluorescens and antibiotic-resistant variants,
101
Pseudomonas stutzeri – Involvement of the
ammonium transporter AmtB in nitrogenase
regulation and ammonium excretion in
Pseudomonas stutzeri A1501, 332
Pseudomonas syringae – Carbon source and
cell density-dependent regulation of type III
secretion system gene expression in
Pseudomonas syringae pathovar tomato
DC3000, 531
purL – Identification of the bacteriocin
subtilosin A and loss of purL results in its
high-level production in Bacillus
amyloliquefaciens, 470
Q
qnrS – First description of the qnrS-like
(qnrS5) gene and analysis of quinolone
resistance-determining regions in motile
Aeromonas spp. from diseased fish and
water, 73
qPCR – Xylo-oligosaccharides inhibit
pathogen adhesion to enterocytes in vitro, 22
QRDR – First description of the qnrS-like
(qnrS5) gene and analysis of quinolone
resistance-determining regions in motile
Aeromonas spp. from diseased fish and
water, 73
Quorum sensing – Complexity of cell–cell
interactions between Pseudomonas sp. AS1
and Acinetobacter oleivorans DR1:
metabolic commensalism, biofilm formation
and quorum quenching, 173
R
R64 plasmid – Neglected but amazingly
diverse type IVb pili, 659
Raman spectroscopy – Biochemical and
genetic characteristics of Cronobacter
sakazakii biofilm formation, 448
 Keyword index / Research in Microbiology 163 (2012) 695–702 701
Rarefaction – Megraft: a software package to
graft ribosomal small subunit (16S/18S)
fragments onto full-length sequences for
accurate species richness and sequencing
depth analysis in pyrosequencing-length
metagenomes and similar environmental
datasets, 407
RDA – Comparative transcriptome analysis of
Paracoccidioides brasiliensis during in
vitro adhesion to type I collagen and
fibronectin: identification of potential
adhesins, 182
rDNA – Megraft: a software package to graft
ribosomal small subunit (16S/18S)
fragments onto full-length sequences for
accurate species richness and sequencing
depth analysis in pyrosequencing-length
metagenomes and similar environmental
datasets, 407
Reactive oxygen species – Polyamines reduce
oxidative stress in Escherichia coli cells
exposed to bactericidal antibiotics, 83
Real-time PCR – Real-time PCR for
Helicobacter pylori quantification and
detection of clarithromycin resistance in
gastric tissue from patients with
gastrointestinal disorders, 109
Regulation – Pili of Gram-positive bacteria:
roles in host colonization, 645
Replication – Structure, replication efficiency
and fragility of yeast ARS elements, 243
Rhizosphere – Influence of nitrogen
fertilization on diazotrophic communities in
the rhizosphere of the Jerusalem artichoke
(Helianthus tuberosus L.), 349 – Impact of
salinity-tolerant MCM6 transgenic tobacco
on soil enzymatic activities and the
functional diversity of rhizosphere microbial
communities, 511
RT-qPCR – Reverse transcriptase real-time
PCR for detection and quantification of
viable Campylobacter jejuni directly from
poultry faecal samples, 64
Rumen – Anaerobic transformation of
octahydro-1,3,5,7-tetranitro-1,3,5,7-
tetrazocine (HMX) by ovine rumen
microorganisms, 567
Ruminococcus gnavus – Aga1, the first alpha-
Galactosidase from the human bacteria
Ruminococcus gnavus E1, efficiently
transcribed in gut conditions, 14
RyhB – Two sRNA RyhB homologs from
Yersinia pestis biovar microtus expressed in
vivo have differential Hfq-dependent
stability, 413
S
Saccharomyces cerevisiae – Structure,
replication efficiency and fragility of yeast
ARS elements, 243
Salmonella Typhimurium – Characterization
of endolysin from a Salmonella
Typhimurium-infecting bacteriophage
SPN1S, 233
Sediment – Nitrate and ammonium uptake by
natural stream sediment microbial
communities in response to nutrient
enrichment, 137
Sediment abiotic properties – Shifts in
phylogenetic diversity of archaeal
communities in mangrove sediments at
different sites and depths in southeastern
Brazil, 366
Sediment microbial community – Shifts in
phylogenetic diversity of archaeal
communities in mangrove sediments at
different sites and depths in southeastern
Brazil, 366
Shigella – Shedding of genes that interfere
with the pathogenic lifestyle: the Shigella
model, 399
Silencing – New regulators of biofilm
development in Candida glabrata, 297
Similarity matrix – Biogeographical diversity
of leaf-associated microbial communities
from salt-secreting Tamarix trees of the
Dead Sea region, 142
Siroheme enzymes – Terminal reduction
reactions of nitrate and sulfate assimilation
in Streptomyces coelicolor A3(2):
identification of genes encoding nitrite and
sulfite reductases, 340
Soil dehydrogenase – Impact of salinity-
tolerant MCM6 transgenic tobacco on soil
enzymatic activities and the functional
diversity of rhizosphere microbial
communities, 511
Species richness analysis – Megraft: a
software package to graft ribosomal small
subunit (16S/18S) fragments onto full-
length sequences for accurate species
richness and sequencing depth analysis in
pyrosequencing-length metagenomes and
similar environmental datasets, 407
Spo0M – The sporulation control gene spo0M
of Bacillus subtilis is a target of the FtsH
metalloprotease, 114
Sporulation – The sporulation control gene
spo0M of Bacillus subtilis is a target of the
FtsH metalloprotease, 114 – Characterization
of sporulation histidine kinases of
Paenibacillus polymyxa, 272
Stable isotopes – Diversity of tailed phages in
Baltic Sea sediment: large number of
siphoviruses with extremely long tails, 292
Staphylococcus aureus – Enhanced activity of
linezolid against Staphylococcus aureus in
cerebrospinal fluid, 157
Staphylococcus epidermidis – Enhanced
activity of linezolid against Staphylococcus
aureus in cerebrospinal fluid, 157
Start-up process – Microbial community
structure stability, a key parameter in
monitoring the development of constructed
wetland mesocosms during start-up, 28
Streptococcus anginosus group – Real-time
monitoring of the adherence of Streptococcus
anginosus group bacteria to extracellular
matrix decorin and biglycan proteoglycans
in biofilm formation, 436
Streptomyces – Streptomyces competition
and co-evolution in relation to plant disease
suppression, 490
Subtilosin A – Identification of the bacteriocin
subtilosin A and loss of purL results in its
high-level production in Bacillus
amyloliquefaciens, 470
Sulfate assimilation – Terminal reduction
reactions of nitrate and sulfate assimilation
in Streptomyces coelicolor A3(2):
identification of genes encoding nitrite and
sulfite reductases, 340
Sulfite reduction – Terminal reduction
reactions of nitrate and sulfate assimilation
in Streptomyces coelicolor A3(2):
identification of genes encoding nitrite and
sulfite reductases, 340
Surface plasmon resonance – Real-time
monitoring of the adherence of Streptococcus
anginosus group bacteria to extracellular
matrix decorin and biglycan proteoglycans
in biofilm formation, 436
Surface receptor – Myxobacterial tools for
social interactions, 579
Survival strategy – Biofilm generation by
Piscirickettsia salmonis under growth stress
conditions: a putative in vivo survival/
persistence strategy in marine environments,
557
Susceptibility – Antibiotic and antimicrobial
peptide combinations: synergistic inhibition
of Pseudomonas fluorescens and antibiotic-
resistant variants, 101
Synergistic effect – Synergistic effect of
antimicrobial peptide arenicin-1 in
combination with antibiotics against
pathogenic bacteria, 479 – Cefoxitin is both
an inhibitor of class A beta-lactamase of
Xanthomonas campestris pv. campestris str.
17 and an inducer of its gene, 550
T
T-RFLP – Influence of nitrogen fertilization
on diazotrophic communities in the
rhizosphere of the Jerusalem artichoke
(Helianthus tuberosus L.), 349
702 Keyword index / Research in Microbiology 163 (2012) 695–702
Tamarix – Biogeographical diversity of leaf-
associated microbial communities from
salt-secreting Tamarix trees of the Dead Sea
region, 142
Tandem repeats – Variability of the tandem
repeat region of the Escherichia coli tolA
gene, 316
TCP – Neglected but amazingly diverse type
IVb pili, 659
Theta replication – Characterization of the
theta replication plasmid pGR7 from
Acetobacter aceti CCM 3610, 419
tolA – Variability of the tandem repeat region
of the Escherichia coli tolA gene, 316
Toxin – Microbial manipulation of the amyloid
fold, 592
Transcription regulation – Carbon source
and cell density-dependent regulation of
type III secretion system gene expression in
Pseudomonas syringae pathovar tomato
DC3000, 531
Transgene – Fate of invading bacteria in soil
and survival of transformants after simulated
uptake of transgenes, as evaluated by a model
system based on lindane degradation, 200
Transgenic plants – Impact of salinity-
tolerant MCM6 transgenic tobacco on soil
enzymatic activities and the functional
diversity of rhizosphere microbial
communities, 511
Tropical mangrove – Shifts in phylogenetic
diversity of archaeal communities in
mangrove sediments at different sites and
depths in southeastern Brazil, 366
Type III secretion – Carbon source and cell
density-dependent regulation of type III
secretion system gene expression in
Pseudomonas syringae pathovar tomato
DC3000, 531
Type IV pili – Physics of bacterial near-
surface motility using flagella and type IV
pili: implications for biofilm formation, 619
– Diversity, assembly and regulation of
archaeal type IV pili-like and non-type-IV
pili-like surface structures, 630,
Myxobacterial tools for social interactions,
579, Neglected but amazingly diverse type
IVb pili, 659
U Weibull analysis – Atomic force and super-
Uncultured viruses – Diversity of tailed phages
in Baltic Sea sediment: large number of
siphoviruses with extremely long tails, 292
Uptake – Nitrate and ammonium uptake by
natural stream sediment microbial
communities in response to nutrient
enrichment, 137
V gene, 550
Variability – Variability of the tandem repeat
region of the Escherichia coli tolA gene, 316
Vector – Attenuated Listeria monocytogenes,
a Mycobacterium tuberculosis ESAT-6
antigen expression and delivery vector for
inducing an immune response, 540
Viriobenthos – Diversity of tailed phages in
Baltic Sea sediment: large number of
siphoviruses with extremely long tails, 292
Virulence – Mutational analysis of
Pseudomonas aeruginosa OxyR to define
the regions required for peroxide resistance
and acute virulence, 55 – Elevated CpxR~P
levels repress the Ysc–Yop type III secretion
system of Yersinia pseudotuberculosis, 518
Virulence genes – Characterization of atypical
Listeria innocua isolated from swine
slaughterhouses and meat markets, 268
W
Wastewaters – Novel gene cassettes and
integrons in antibiotic-resistant bacteria
isolated from urban wastewaters, 92
resolution microscopy support a role for
LapA as a cell-surface biofilm adhesin of
Pseudomonas fluorescens, 685
X
Xanthomonas campestris pv. campestris –
Cefoxitin is both an inhibitor of class A
beta-lactamase of Xanthomonas campestris
pv. campestris str. 17 and an inducer of its
Y
Yarrowia lipolytica – Identification of
dimorphism-involved genes of Yarrowia
lipolytica by means of microarray analysis,
378
Yersinia pestis – Two sRNA RyhB homologs
from Yersinia pestis biovar microtus
expressed in vivo have differential Hfq-
dependent stability, 413