Research in Microbiology 167 (2016) 792–800
www.elsevier.com/locate/resmic
1 Acidibacillus – Isolation and characterisation
1-Aminocyclopropane-1-carboxylate (ACC)
deaminase – Detection of biosynthetic
gene and phytohormone production by
endophytic actinobacteria associated with
Solanum lycopersicum and their plant-
growth-promoting effect, 692
1,2,4-Triazole-ciprofloxacin hybrid
– Inhibitory effect of 1,2,4-triazole-
ciprofloxacin hybrids on Haemophilus
parainfluenzae and Haemophilus influenzae
biofilm formation in vitro under stationary
conditions, 647
5 anaerobic elemental sulfur oxidation with
51V
NMR – 51V NMR investigation of cell-
associated vanadate species in Phycomyces
blakesleeanus mycelium, 521
A oxidizing Acidithiobacillus ferrooxidans
Abundance – Occurrence of Stenotrophomonas
maltophilia in agricultural soils and
antibiotic resistance properties, 313
Acanthamoeba castellanii – DVC-FISH
and PMA-qPCR techniques to assess the
survival of Helicobacter pylori inside
Acanthamoeba castellanii, 29
Acetobacter – Characterization of newly
identified DnaA and DnaB proteins from
Acetobacter, 655
Acid stress – Life in heaps: a review of
microbial responses to variable acidity in
sulfide mineral bioleaching heaps for metal
extraction, 576
Acid tolerance – The arginine deiminase
system facilitates environmental adaptability
of Streptococcus equi ssp. zooepidemicus
through pH adjustment, 403 – Metabolic
parameters linked by phenotype microarray
to acid resistance profiles of poultry-
associated Salmonella enterica, 745
Acidianus – Saline-water bioleaching of
chalcopyrite with thermophilic, iron(II)-
and sulfur-oxidizing microorganisms, 546
Acidianus spp. – Biofilm formation and
interspecies interactions in mixed cultures
of thermo-acidophilic archaea Acidianus
spp. and Sulfolobus metallicus, 604
0923–2508/2016
doi:10.1016/S0923-2508(16)30130-9
Keyword index
of mineral-oxidising “Acidibacillus”
spp. from mine sites and geothermal
environments in different global locations,
613
Acidithiobacillus ferrooxidans – Comparative
proteomics of Acidithiobacillus
ferrooxidans grown in the presence and
absence of uranium, 234 – Are there multiple
mechanisms of anaerobic sulfur oxidation
with ferric iron in Acidithiobacillus
ferrooxidans?, 357 – Comparative
proteomic analysis of sulfur-oxidizing
Acidithiobacillus ferrooxidans CCM 4253
cultures having lost the ability to couple
ferric iron reduction, 587
Acidithiobacillus – Detection, identification
and typing of Acidithiobacillus species and
strains: a review, 555
Acidophile – Comparative proteomics of
Acidithiobacillus ferrooxidans grown in the
presence and absence of uranium, 234 –
Genomic and metagenomic challenges and
opportunities for bioleaching: a mini-review,
529 – Detection, identification and typing
of Acidithiobacillus species and strains: a
review, 555 – Electricity generation from
an inorganic sulfur compound containing
mining wastewater by acidophilic
microorganisms, 568 – Life in heaps: a
review of microbial responses to variable
acidity in sulfide mineral bioleaching
heaps for metal extraction, 576 – Microbial
community profiling of the Chinoike Jigoku
(“Blood Pond Hell”) hot spring in Beppu,
Japan: isolation and characterization of
Fe(III)-reducing Sulfolobus sp. strain GA1,
595 – Isolation and characterisation of
mineral-oxidising “Acidibacillus” spp. from
mine sites and geothermal environments in
different global locations, 613
Actinobacteria – Codon usage bias in phylum
Actinobacteria: relevance to environmental
adaptation and host pathogenicity, 669
Adaptation – Alternative scenarios
of starvation-induced adaptation in
Pectobacterium atrosepticum, 254
Aerobic growth conditions – H2 production
in Rhodopseudomonas palustris as a way to
cope with high light intensities, 350
Aerobic/anaerobic – A discrete role for FNR
in the transcriptional response to moderate
changes in oxygen by Haemophilus
influenzae Rd KW20, 103
Alps – Spatial and temporal variability of
bacterial communities in high alpine water
spring sediments, 325
Ammonia – The arginine deiminase system
facilitates environmental adaptability of
Streptococcus equi ssp. zooepidemicus
through pH adjustment, 403
Anaerobic growth conditions – H2 production
in Rhodopseudomonas palustris as a way to
cope with high light intensities, 350
Anaerobic respiration pathway – Are
there multiple mechanisms of anaerobic
sulfur oxidation with ferric iron in
Acidithiobacillus ferrooxidans?, 357 –
Comparative proteomic analysis of sulfur-
CCM 4253 cultures having lost the ability to
couple anaerobic elemental sulfur oxidation
with ferric iron reduction, 587
Antagonistic traits, PGP – Detection of
biosynthetic gene and phytohormone
production by endophytic actinobacteria
associated with Solanum lycopersicum and
their plant-growth-promoting effect, 692
Anthranilate – Burkholderia pseudomallei
kynB plays a role in AQ production,
biofilm formation, bacterial swarming and
persistence, 159
Anti-biofilm and anti-adhesive activity
– Inhibitory effect of 1,2,4-triazole-
ciprofloxacin hybrids on Haemophilus
parainfluenzae and Haemophilus influenzae
biofilm formation in vitro under stationary
conditions, 647
Antibiotic – The cyclic AMP receptor
protein (CRP) regulates mqsRA, coding
for the bacterial toxin-antitoxin gene pair,
in Escherichia coli, 58 – Improved in
vitro evaluation of novel antimicrobials:
potential synergy between human plasma
and antibacterial peptidomimetics, AMPs
and antibiotics against human pathogenic
bacteria, 72 – Significant antibacterial
activity and synergistic effects of camel
lactoferrin with antibiotics against
methicillin-resistant Staphylococcus aureus
(MRSA), 480
 Keyword index / Research in Microbiology 167 (2016) 792–800
Antibiotic resistance – Occurrence
of Stenotrophomonas maltophilia in
agricultural soils and antibiotic resistance
properties, 313 – Use of phenotype
microarrays to study the effect of acquisition
of resistance to antimicrobials in bacterial
physiology, 723
Antibiotic tolerance – Burkholderia
pseudomallei kynB plays a role in AQ
production, biofilm formation, bacterial
swarming and persistence, 159
Antifungal activity – A rifampicin-resistant
(rpoB) mutation in Pseudomonas protegens
Pf-5 strain leads to improved antifungal
activity and elevated production of
secondary metabolites, 625
Antifungal lipopeptides – The Tunisian
oasis ecosystem is a source of antagonistic
Bacillus spp. producing diverse antifungal
lipopeptides, 46
Antimicrobial compounds – Novel
components of leaf bacterial communities of
field-grown tomato plants and their potential
for plant growth promotion and biocontrol
of tomato diseases, 222 – Antimicrobial
compounds from endophytic Streptomyces
sp. BCC72023 isolated from rice (Oryza
sativa L.), 290 – The antimicrobial potential
of algicolous marine fungi for counteracting
multidrug-resistant bacteria: phylogenetic
diversity and chemical profiling, 492
Antimicrobial peptide – Improved in
vitro evaluation of novel antimicrobials:
potential synergy between human plasma
and antibacterial peptidomimetics, AMPs
and antibiotics against human pathogenic
bacteria, 72 – Expression of essential genes
for biosynthesis of antimicrobial peptides of
Bacillus is modulated by inactivated cells
of target microorganisms, 83 – Insights
into aureocin A70 regulation: participation
of regulator AurR, alternative transcription
factor ␴B and phage ␾11 regulator cI, 90
Arginine – The arginine deiminase system
facilitates environmental adaptability of
Streptococcus equi ssp. zooepidemicus
through pH adjustment, 403
Arginine deiminase system – The arginine
deiminase system facilitates environmental
adaptability of Streptococcus equi ssp.
zooepidemicus through pH adjustment, 403
ARISA – Spatial and temporal variability of
bacterial communities in high alpine water
spring sediments, 325
Artworks – Connecting phenome to genome
in Pseudomonas stutzeri 5190: an artwork
biocleaning bacterium, 757
Atopobium – A DNA tool for early detection
of vaginal dysbiosis in African women, 133
ATP binding – The Walker A motif mutation
recA4159 abolishes the SOS response and
recombination in a recA730 mutant of
Escherichia coli, 462
Auxiliary proteins – Efficient respiration on
TMAO requires TorD and TorE auxiliary
proteins in Shewanella oneidensis, 630
Azospirillum – Influence of tryptophan and
indole-3-acetic acid on starch accumulation
in the synthetic mutualistic Chlorella
sorokiniana – Azospirillum brasilense
system under heterotrophic conditions, 367
Azospirillum brasilense – The cyclic-di-GMP
diguanylate cyclase CdgA has a role in
biofilm formation and exopolysaccharide
production in Azospirillum brasilense, 190
B characterizing functional alkane degraders
Bacillus – The Tunisian oasis ecosystem
is a source of antagonistic Bacillus spp.
producing diverse antifungal lipopeptides,
46 – Expression of essential genes for
biosynthesis of antimicrobial peptides of
Bacillus is modulated by inactivated cells of
target microorganisms, 83
Bacillus licheniformis WX-02 – Construction
and analysis of a genome-scale metabolic
network for Bacillus licheniformis WX-02,
282
Bacillus subtilis – Mismatch repair in Gram-
positive bacteria, 4 – Septal localization
by membrane targeting sequences and a
conserved sequence essential for activity
at the COOH-terminus of Bacillus subtilis
cardiolipin synthase, 202 – Influence of
promoters on the production of fengycin in
Bacillus spp., 272
Bacteria – Spatial and temporal variability of
bacterial communities in high alpine water
spring sediments, 325
Bacterial metabolism – Identification and
differential production of ubiquinone-8
in the bacterial predator Bdellovibrio
bacteriovorus, 413
Bacterial vaginosis – A DNA tool for early
detection of vaginal dysbiosis in African
women, 133
Bacterial virulence – Use of phenotype
microarrays to study the effect of acquisition
of resistance to antimicrobials in bacterial
physiology, 723
Bacteriocin – Insights into aureocin A70
regulation: participation of regulator AurR,
alternative transcription factor ␴B and phage
␾11 regulator cI, 90 – A ptsP deficiency
in PGPR Pseudomonas fluorescens SF39a
affects bacteriocin production and bacterial
fitness in the wheat rhizosphere, 178
Bacteriophage – Propagation method for
persistent high yield of diverse Listeria
phages on permissive hosts at refrigeration
temperatures, 685
Bioactive fungal compounds – The
antimicrobial potential of algicolous
marine fungi for counteracting multidrug-
resistant bacteria: phylogenetic diversity
and chemical profiling, 492
793
Biocides – Use of phenotype microarrays to
study the effect of acquisition of resistance
to antimicrobials in bacterial physiology,
723
Biocleaning – Connecting phenome to
genome in Pseudomonas stutzeri 5190: an
artwork biocleaning bacterium, 757
Biocontrol – Novel components of leaf
bacterial communities of field-grown
tomato plants and their potential for plant
growth promotion and biocontrol of tomato
diseases, 222
Biodegradation – Separating and
from crude-oil-contaminated sites via
magnetic nanoparticle-mediated isolation,
731
Biofilm – Construction and phenotypic
characterization of M68, an RruI
quorum sensing knockout mutant of the
photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380 – A dual-
species microbial model for studying the
dynamics between oral streptococci and
periodontal pathogens during biofilm
development on titanium surfaces by flow
cytometry, 393 – Biofilm formation and
interspecies interactions in mixed cultures
of thermo-acidophilic archaea Acidianus
spp. and Sulfolobus metallicus, 604
Biofilm production – The cyclic-di-GMP
diguanylate cyclase CdgA has a role in
biofilm formation and exopolysaccharide
production in Azospirillum brasilense, 190
Biohydrometallurgy – Lessons learned from
thirty years of geomicrobiological studies of
Río Tinto, 539
Bioinformatics – Genomic and metagenomic
challenges and opportunities for
bioleaching: a mini-review, 529
Bioleaching – Genomic and metagenomic
challenges and opportunities for
bioleaching: a mini-review, 529 – Detection,
identification and typing of Acidithiobacillus
species and strains: a review, 555
BIOLOG PM plate – Separating and
characterizing functional alkane degraders
from crude-oil-contaminated sites via
magnetic nanoparticle-mediated isolation,
731
Biological control – The Tunisian oasis
ecosystem is a source of antagonistic
Bacillus spp. producing diverse antifungal
lipopeptides, 46 – Expression of essential
genes for biosynthesis of antimicrobial
peptides of Bacillus is modulated by
inactivated cells of target microorganisms,
83
Biomining – Genomic and metagenomic
challenges and opportunities for
bioleaching: a mini-review, 529
Biotechnology – Propagation method for
persistent high yield of diverse Listeria
phages on permissive hosts at refrigeration
temperatures, 685
794
␤-lactams – Potentialization of ␤-lactams
with colistin: in case of extended spectrum
␤-lactamase producing Escherichia coli
strains isolated from children with urinary
infections, 215
Botrytis cinerea – Novel components of
leaf bacterial communities of field-grown
tomato plants and their potential for plant
growth promotion and biocontrol of tomato
diseases, 222
bZIP domain – A novel bZIP transcription
factor ClrC positively regulates multiple
stress responses, conidiation and cellulase
expression in Penicillium oxalicum, 424
C Helicobacter pylori inside Acanthamoeba
Campylobacter jejuni – Ex vivo proteomics
of Campylobacter jejuni 81-176 reveal that
FabG affects fatty acid composition to alter
bacterial growth fitness in the chicken gut,
63
Cell phase – Phase-dependent dynamics of
the lac promoter under nutrient stress, 451
Cellulolytic enzyme – A novel bZIP
transcription factor ClrC positively regulates
multiple stress responses, conidiation
and cellulase expression in Penicillium
oxalicum, 424
Cell-wall-deficient forms – Alternative
scenarios of starvation-induced adaptation
in Pectobacterium atrosepticum, 254
Characterization – Diversity of yeasts
associated with the sea surface microlayer
and underlying water along the northern
coast of Taiwan, 35
Chemolitho-heterotrophs – Isolation and
characterisation of mineral-oxidising
“Acidibacillus” spp. from mine sites and
geothermal environments in different global
locations, 613
Chemolithotrophs – Life in heaps: a review
of microbial responses to variable acidity in
sulfide mineral bioleaching heaps for metal
extraction, 576
Chicken colonization – Ex vivo proteomics
of Campylobacter jejuni 81-176 reveal that
FabG affects fatty acid composition to alter
bacterial growth fitness in the chicken gut,
63
Chickpea endophytes – Association of plant
growth-promoting Serratia spp. with the
root nodules of chickpea, 510
Chlorella – Influence of tryptophan and
indole-3-acetic acid on starch accumulation
in the synthetic mutualistic Chlorella
sorokiniana – Azospirillum brasilense
system under heterotrophic conditions, 367
CL synthase – Septal localization by
membrane targeting sequences and a
conserved sequence essential for activity
at the COOH-terminus of Bacillus subtilis
cardiolipin synthase, 202
Keyword index / Research in Microbiology 167 (2016) 792–800
Clinical mastitis – Genetic diversity, the
virulence gene profile and antimicrobial
resistance of clinical mastitis-associated
Escherichia coli, 678
clrC – A novel bZIP transcription factor
ClrC positively regulates multiple stress
responses, conidiation and cellulase
expression in Penicillium oxalicum, 424
ClsA – Septal localization by membrane
targeting sequences and a conserved
sequence essential for activity at the COOH-
terminus of Bacillus subtilis cardiolipin
synthase, 202
Co-culture – DVC-FISH and PMA-qPCR
techniques to assess the survival of
castellanii, 29
Codon adaptation index – Codon usage
bias in phylum Actinobacteria: relevance
to environmental adaptation and host
pathogenicity, 669
Codon usage – Codon usage bias in phylum
Actinobacteria: relevance to environmental
adaptation and host pathogenicity, 669
Colistin – Potentialization of ␤-lactams with
colistin: in case of extended spectrum
␤-lactamase producing Escherichia coli
strains isolated from children with urinary
infections, 215
Competitiveness – A ptsP deficiency in
PGPR Pseudomonas fluorescens SF39a
affects bacteriocin production and bacterial
fitness in the wheat rhizosphere, 178
Complementation – Identification and
functional annotation of mycobacterial
septum formation genes using cell division
mutants of Escherichia coli, 142
Corynebacterium – Involvement of the osrR
gene in the hydrogen peroxide-mediated
stress response of Corynebacterium
glutamicum, 20
CRP – The cyclic AMP receptor protein
(CRP) regulates mqsRA, coding for the
bacterial toxin-antitoxin gene pair, in
Escherichia coli, 58
Cr(VI) reduction – Microbial community
profiling of the Chinoike Jigoku (“Blood
Pond Hell”) hot spring in Beppu, Japan:
isolation and characterization of Fe(III)-
reducing Sulfolobus sp. strain GA1, 595
Cyclic di-GMP – The cyclic-di-GMP
diguanylate cyclase CdgA has a role in
biofilm formation and exopolysaccharide
production in Azospirillum brasilense, 190
D compounds from endophytic Streptomyces
Date palm rhizosphere – The Tunisian
oasis ecosystem is a source of antagonistic
Bacillus spp. producing diverse antifungal
lipopeptides, 46
Decline – Evidence of metabolically active but
non-culturable Listeria monocytogenes in
long-term growth at 10 °C, 334
Dietary formulations – Diet drives quick
changes in the metabolic activity and
composition of human gut microbiota in a
validated in vitro gut model, 114
Diguanylate cyclase activity – The cyclic-di-
GMP diguanylate cyclase CdgA has a role
in biofilm formation and exopolysaccharide
production in Azospirillum brasilense, 190
Distribution – Occurrence of
Stenotrophomonas maltophilia in
agricultural soils and antibiotic resistance
properties, 313
Diversity – Detection, identification and
typing of Acidithiobacillus species and
strains: a review, 555
Divisome assembly – Identification and
functional annotation of mycobacterial
septum formation genes using cell division
mutants of Escherichia coli, 142
DnaA protein – Characterization of newly
identified DnaA and DnaB proteins from
Acetobacter, 655
DnaB protein – Characterization of newly
identified DnaA and DnaB proteins from
Acetobacter, 655
DVC-FISH – DVC-FISH and PMA-qPCR
techniques to assess the survival of
Helicobacter pylori inside Acanthamoeba
castellanii, 29
E
Effective number of codons – Codon usage
bias in phylum Actinobacteria: relevance
to environmental adaptation and host
pathogenicity, 669
Efomycins – Antimicrobial compounds from
endophytic Streptomyces sp. BCC72023
isolated from rice (Oryza sativa L.), 290
Electricity generation – Electricity
generation from an inorganic sulfur
compound containing mining wastewater
by acidophilic microorganisms, 568
Electron transport – Identification and
differential production of ubiquinone-8
in the bacterial predator Bdellovibrio
bacteriovorus, 413
Endophytic actinobacteria – Detection
of biosynthetic gene and phytohormone
production by endophytic actinobacteria
associated with Solanum lycopersicum and
their plant-growth-promoting effect, 692
Endophytic actinomycete – Antimicrobial
sp. BCC72023 isolated from rice (Oryza
sativa L.), 290
Endophytic culturable bacteria – Novel
components of leaf bacterial communities
of field-grown tomato plants and their
potential for plant growth promotion and
biocontrol of tomato diseases, 222
 Keyword index / Research in Microbiology 167 (2016) 792–800
Environmental fitness – RpoS differentially
affects the general stress response and
biofilm formation in the endophytic Serratia
plymuthica G3, 168
Environmental – Environmental Legionella
spp. collected in urban test sites of South
East Queensland, Australia, are virulent to
human macrophages in vitro, 149
Erwinia chrysanthemi – Regulation of pel
genes, major virulence factors in the plant
pathogen bacterium Dickeya dadantii, is
mediated by cooperative binding of the
nucleoid-associated protein H-NS, 247
ESBL – Potentialization of ␤-lactams with
colistin: in case of extended spectrum
␤-lactamase producing Escherichia coli
strains isolated from children with urinary
infections, 215
ESBL-producing Escherichia coli – Heat
resistance in extended-spectrum beta-
lactamase-producing Escherichia coli may
favor environmental survival in a hospital
setting, 345
Escherichia coli – The cyclic AMP receptor
protein (CRP) regulates mqsRA, coding
for the bacterial toxin-antitoxin gene pair,
in Escherichia coli, 58 – Identification
and functional annotation of mycobacterial
septum formation genes using cell division
mutants of Escherichia coli, 142 –
Potentialization of ␤-lactams with colistin:
in case of extended spectrum ␤-lactamase
producing Escherichia coli strains isolated
from children with urinary infections,
215 – Metastable coexistence of multiple
genotypes in a constant environment with
a single resource through fixed settings of
a multiplication-survival trade-off, 240 –
Genetic diversity, the virulence gene profile
and antimicrobial resistance of clinical
mastitis-associated Escherichia coli, 678
Excess reducing power – H2 production in
Rhodopseudomonas palustris as a way to
cope with high light intensities, 350
Exoenzymes – RpoS differentially affects
the general stress response and biofilm
formation in the endophytic Serratia
plymuthica G3, 168
Extreme environment – Microbial community
profiling of the Chinoike Jigoku (“Blood
Pond Hell”) hot spring in Beppu, Japan:
isolation and characterization of Fe(III)-
reducing Sulfolobus sp. strain GA1, 595
F Flux balance analysis – Construction and
Fatty acid biosynthesis – Ex vivo proteomics
of Campylobacter jejuni 81-176 reveal that
FabG affects fatty acid composition to alter
bacterial growth fitness in the chicken gut,
63
Fe(III) reduction – Microbial community
profiling of the Chinoike Jigoku (“Blood
Pond Hell”) hot spring in Beppu, Japan:
isolation and characterization of Fe(III)-
reducing Sulfolobus sp. strain GA1, 595
Fengycin – Influence of promoters on the
production of fengycin in Bacillus spp., 272
Fermentation – Diet drives quick changes in
the metabolic activity and composition of
human gut microbiota in a validated in vitro
gut model, 114
Ferric iron reduction – Are there multiple
mechanisms of anaerobic sulfur oxidation
with ferric iron in Acidithiobacillus
ferrooxidans?, 357 – Comparative
proteomic analysis of sulfur-oxidizing
Acidithiobacillus ferrooxidans CCM 4253
cultures having lost the ability to couple
anaerobic elemental sulfur oxidation with
ferric iron reduction, 587
Filament formation – The Walker A motif
mutation recA4159 abolishes the SOS
response and recombination in a recA730
mutant of Escherichia coli, 462
Fingerprinting – Spatial and temporal
variability of bacterial communities in
high alpine water spring sediments, 325
– Detection, identification and typing of
Acidithiobacillus species and strains: a
review, 555
Fitness costs – Use of phenotype microarrays
to study the effect of acquisition of
resistance to antimicrobials in bacterial
physiology, 723
Flagella – Elucidation of the functional role
of flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262
fliI – Elucidation of the functional role of
flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262
fliJ – Elucidation of the functional role of
flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262
Flow cytometry – A dual-species microbial
model for studying the dynamics between
oral streptococci and periodontal pathogens
during biofilm development on titanium
surfaces by flow cytometry, 393
Fluorescence cytometry – Evidence of
metabolically active but non-culturable
Listeria monocytogenes in long-term
growth at 10 °C, 334
analysis of a genome-scale metabolic
network for Bacillus licheniformis WX-02,
282
FNR – A discrete role for FNR in the
transcriptional response to moderate
changes in oxygen by Haemophilus
influenzae Rd KW20, 103
Food safety – Propagation method for
persistent high yield of diverse Listeria
phages on permissive hosts at refrigeration
795
temperatures, 685 – Metabolic parameters
linked by phenotype microarray to acid
resistance profiles of poultry-associated
Salmonella enterica, 745
Functional alkane degraders – Separating
and characterizing functional alkane
degraders from crude-oil-contaminated
sites via magnetic nanoparticle-mediated
isolation, 731
Functional diversity – Phenotype
MicroArray™ system in the study of fungal
functional diversity and catabolic versatility,
710
Fungal ecology – Phenotype MicroArray™
system in the study of fungal functional
diversity and catabolic versatility, 710
Fungi – 51V NMR investigation of cell-
associated vanadate species in Phycomyces
blakesleeanus mycelium, 521 – Phenotype
MicroArray™ system in the study of fungal
functional diversity and catabolic versatility,
710
G
Gardnerella – A DNA tool for early detection
of vaginal dysbiosis in African women, 133
Gene expression – Identification and
differential production of ubiquinone-8
in the bacterial predator Bdellovibrio
bacteriovorus, 413
Genome – Connecting phenome to genome
in Pseudomonas stutzeri 5190: an artwork
biocleaning bacterium, 757
Genome resequencing – A single amino acid
mutation in Spo0A results in sporulation
deficiency of Paenibacillus polymyxa SC2,
472
Genomics – Genomic and metagenomic
challenges and opportunities for
bioleaching: a mini-review, 529
Geomicrobiology – Lessons learned from
thirty years of geomicrobiological studies
of Río Tinto, 539
GFP expression – Influence of promoters
on the production of fengycin in Bacillus
spp., 272
Growth promotion – Novel components of
leaf bacterial communities of field-grown
tomato plants and their potential for plant
growth promotion and biocontrol of tomato
diseases, 222
H
Helicobacter pylori – DVC-FISH and PMA-
qPCR techniques to assess the survival of
Helicobacter pylori inside Acanthamoeba
castellanii, 29
H2-producing conditions – H2 production in
Rhodopseudomonas palustris as a way to
cope with high light intensities, 350
796
Haemophilus influenzae – Haemophilus
influenzae strains possess variations in the
global transcriptional profile in response
to oxygen levels and this influences
sensitivity to environmental stresses, 13 – A
discrete role for FNR in the transcriptional
response to moderate changes in oxygen
by Haemophilus influenzae Rd KW20, 103
Haemophilus spp. – Inhibitory effect of
1,2,4-triazole-ciprofloxacin hybrids
on Haemophilus parainfluenzae and
Haemophilus influenzae biofilm formation
in vitro under stationary conditions, 647
HdtS – Construction and phenotypic
characterization of M68, an RruI
quorum sensing knockout mutant of the
photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380
Heat resistance – Heat resistance in extended-
spectrum beta-lactamase-producing
Escherichia coli may favor environmental
survival in a hospital setting, 345
Highly expressed genes – Codon usage
bias in phylum Actinobacteria: relevance
to environmental adaptation and host
pathogenicity, 669
H-NS/ Virulence genes – Regulation of pel
genes, major virulence factors in the plant
pathogen bacterium Dickeya dadantii, is
mediated by cooperative binding of the
nucleoid-associated protein H-NS, 247
Hydrochemistry – Spatial and temporal
variability of bacterial communities in high
alpine water spring sediments, 325
I and synergistic effects of camel lactoferrin
IAA-lysine synthase – Indole-3-acetic acid in
plant–pathogen interactions: a key molecule
for in planta bacterial virulence and fitness,
774
iaaM – Detection of biosynthetic gene and
phytohormone production by endophytic
actinobacteria associated with Solanum
lycopersicum and their plant-growth-
promoting effect, 692
Iberian Pyrite Belt – Lessons learned from
thirty years of geomicrobiological studies
of Río Tinto, 539
In vitro techniques – Diet drives quick
changes in the metabolic activity and
composition of human gut microbiota in a
validated in vitro gut model, 114
Indole-3-acetic acid – RpoS differentially
affects the general stress response and
biofilm formation in the endophytic
Serratia plymuthica G3, 168 – Influence
of tryptophan and indole-3-acetic acid
on starch accumulation in the synthetic
mutualistic Chlorella sorokiniana –
Azospirillum brasilense system under
heterotrophic conditions, 367 – Association
of plant growth-promoting Serratia spp.
with the root nodules of chickpea, 510
– Indole-3-acetic acid in plant–pathogen
interactions: a key molecule for in planta
bacterial virulence and fitness, 774
Keyword index / Research in Microbiology 167 (2016) 792–800
Interspecies interactions – Biofilm formation
and interspecies interactions in mixed
cultures of thermo-acidophilic archaea
Acidianus spp. and Sulfolobus metallicus,
604
Iron deficiency – Iron deficiency resistance
mechanisms enlightened by gene expression
analysis in Paenibacillus riograndensis
SBR5, 501
Iron oxidation – Isolation and characterisation
of mineral-oxidising “Acidibacillus”
spp. from mine sites and geothermal
environments in different global locations,
613
Isolation – Diversity of yeasts associated with
the sea surface microlayer and underlying
water along the northern coast of Taiwan, 35
Iturin – Expression of essential genes for
biosynthesis of antimicrobial peptides of
Bacillus is modulated by inactivated cells of
target microorganisms, 83
K
Kynurenine – Burkholderia pseudomallei
kynB plays a role in AQ production,
biofilm formation, bacterial swarming and
persistence, 159
L Metabolic activity – Evidence of
Lactobacillus – A DNA tool for early detection
of vaginal dysbiosis in African women, 133
Lactoferrin – Significant antibacterial activity
with antibiotics against methicillin-resistant
Staphylococcus aureus (MRSA), 480
LC–MS – Ex vivo proteomics of
Campylobacter jejuni 81-176 reveal that
FabG affects fatty acid composition to alter
bacterial growth fitness in the chicken gut,
63
Legionella – Environmental Legionella spp.
collected in urban test sites of South East
Queensland, Australia, are virulent to
human macrophages in vitro, 149
Listeria monocytogenes – Evidence of
metabolically active but non-culturable
Listeria monocytogenes in long-term
growth at 10 °C, 334 – Propagation method
for persistent high yield of diverse Listeria
phages on permissive hosts at refrigeration
temperatures, 685
Long-term survival – Evidence of
metabolically active but non-culturable
Listeria monocytogenes in long-term
growth at 10 °C, 334
Low shear environment – Construction and
phenotypic characterization of M68, an
RruI quorum sensing knockout mutant of
the photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380
M
Macrolides – Antimicrobial compounds from
endophytic Streptomyces sp. BCC72023
isolated from rice (Oryza sativa L.), 290
Magnetic nanoparticle-mediated
isolation – Separating and characterizing
functional alkane degraders from crude-
oil-contaminated sites via magnetic
nanoparticle-mediated isolation, 731
Marine fungi – The antimicrobial potential of
algicolous marine fungi for counteracting
multidrug-resistant bacteria: phylogenetic
diversity and chemical profiling, 492
Marine natural products – The antimicrobial
potential of algicolous marine fungi for
counteracting multidrug-resistant bacteria:
phylogenetic diversity and chemical
profiling, 492
MELiSSA – Construction and phenotypic
characterization of M68, an RruI
quorum sensing knockout mutant of the
photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380
Membrane targeting sequence – Septal
localization by membrane targeting
sequences and a conserved sequence
essential for activity at the COOH-terminus
of Bacillus subtilis cardiolipin synthase,
202
metabolically active but non-culturable
Listeria monocytogenes in long-term
growth at 10 °C, 334
Metabolic network – Construction and
analysis of a genome-scale metabolic
network for Bacillus licheniformis WX-02,
282
Metabolic resistance – Haemophilus
influenzae strains possess variations in the
global transcriptional profile in response to
oxygen levels and this influences sensitivity
to environmental stresses, 13
Metabolism – Metabolic parameters linked
by phenotype microarray to acid resistance
profiles of poultry-associated Salmonella
enterica, 745
Metagenomics – Metagenomes provide
valuable comparative information on soil
microeukaryotes, 436 – Genomic and
metagenomic challenges and opportunities
for bioleaching: a mini-review, 529
Metal resistance – Occurrence of
Stenotrophomonas maltophilia in
agricultural soils and antibiotic resistance
properties, 313
Metallosphaera – Saline-water bioleaching
of chalcopyrite with thermophilic, iron(II)-
and sulfur-oxidizing microorganisms, 546
Microbial diversity – Microbial community
profiling of the Chinoike Jigoku (“Blood
Pond Hell”) hot spring in Beppu, Japan:
isolation and characterization of Fe(III)-
reducing Sulfolobus sp. strain GA1, 595
 Keyword index / Research in Microbiology 167 (2016) 792–800
Microbial fuel cell – Electricity generation
from an inorganic sulfur compound
containing mining wastewater by acidophilic
microorganisms, 568
Microbial invasion – Fungal communities
as an experimental approach to Darwin's
naturalization hypothesis, 126
Microbiota – Diet drives quick changes in
the metabolic activity and composition of
human gut microbiota in a validated in vitro
gut model, 114
Microbiota profiling – Diet drives quick
changes in the metabolic activity and
composition of human gut microbiota in a
validated in vitro gut model, 114
Microeukaryote – Metagenomes provide
valuable comparative information on soil
microeukaryotes, 436
Mining – Electricity generation from an
inorganic sulfur compound containing
mining wastewater by acidophilic
microorganisms, 568
Mismatch repair – Mismatch repair in Gram-
positive bacteria, 4
MLST – Genetic diversity, the virulence
gene profile and antimicrobial resistance
of clinical mastitis-associated Escherichia
coli, 678
Molybdoenzyme maturation – Efficient
respiration on TMAO requires TorD and
TorE auxiliary proteins in Shewanella
oneidensis, 630
Motility – Elucidation of the functional role
of flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262
mqsR – The cyclic AMP receptor protein
(CRP) regulates mqsRA, coding for the
bacterial toxin-antitoxin gene pair, in
Escherichia coli, 58
mRNA variation – Phase-dependent
dynamics of the lac promoter under nutrient
stress, 451
MRSA – Significant antibacterial activity
and synergistic effects of camel lactoferrin
with antibiotics against methicillin-resistant
Staphylococcus aureus (MRSA), 480
Multidrug and toxic compound extrusion
(MATE) – Indole-3-acetic acid in plant–
pathogen interactions: a key molecule for
in planta bacterial virulence and fitness, 774
Multidrug-resistant bacteria – The
antimicrobial potential of algicolous
marine fungi for counteracting multidrug-
resistant bacteria: phylogenetic diversity
and chemical profiling, 492
MutL – Mismatch repair in Gram-positive
bacteria, 4
MutS – Mismatch repair in Gram-positive
bacteria, 4
Mycobacterium smegmatis – Identification
and functional annotation of mycobacterial
septum formation genes using cell division
mutants of Escherichia coli, 142
Mycobacterium tuberculosis – Identification
and functional annotation of mycobacterial
septum formation genes using cell division
mutants of Escherichia coli, 142
N gene expression analysis in Paenibacillus
n-Alkane – Separating and characterizing
functional alkane degraders from crude-
oil-contaminated sites via magnetic
nanoparticle-mediated isolation, 731
New species – Diversity of yeasts associated
with the sea surface microlayer and
underlying water along the northern coast
of Taiwan, 35
Nosocomial infection – Heat resistance
in extended-spectrum beta-lactamase-
producing Escherichia coli may favor
environmental survival in a hospital setting,
345
Novel species – Isolation and characterisation
of mineral-oxidising “Acidibacillus”
spp. from mine sites and geothermal
environments in different global locations,
613
Nucleoid condensation – Alternative
scenarios of starvation-induced adaptation
in Pectobacterium atrosepticum, 254
Nucleoid-associated rrotein – Regulation of
pel genes, major virulence factors in the
plant pathogen bacterium Dickeya dadantii,
is mediated by cooperative binding of the
nucleoid-associated protein H-NS, 247
Nutrient stress – Phase-dependent dynamics
of the lac promoter under nutrient stress,
451
O
Oasis ecosystem – The Tunisian oasis
ecosystem is a source of antagonistic
Bacillus spp. producing diverse antifungal
lipopeptides, 46
Oral streptococci – A dual-species microbial
model for studying the dynamics between
oral streptococci and periodontal pathogens
during biofilm development on titanium
surfaces by flow cytometry, 393
Osmotic stress – Saline-water bioleaching
of chalcopyrite with thermophilic, iron(II)-
and sulfur-oxidizing microorganisms, 546
Oxidative stress – Haemophilus influenzae
strains possess variations in the global
transcriptional profile in response to oxygen
levels and this influences sensitivity to
environmental stresses, 13 – Involvement
of the osrR gene in the hydrogen
peroxide-mediated stress response of
Corynebacterium glutamicum, 20 – A
discrete role for FNR in the transcriptional
response to moderate changes in oxygen
by Haemophilus influenzae Rd KW20, 103
797
Oxygen metabolism – Haemophilus
influenzae strains possess variations in the
global transcriptional profile in response to
oxygen levels and this influences sensitivity
to environmental stresses, 13
P
Paenibacillus genus – Iron deficiency
resistance mechanisms enlightened by
riograndensis SBR5, 501
Paenibacillus polymyxa – A single amino acid
mutation in Spo0A results in sporulation
deficiency of Paenibacillus polymyxa SC2,
472
Pathogen – Genetic diversity, the virulence
gene profile and antimicrobial resistance
of clinical mastitis-associated Escherichia
coli, 678
Pathogenicity – Environmental Legionella
spp. collected in urban test sites of South
East Queensland, Australia, are virulent
to human macrophages in vitro, 149
– Elucidation of the functional role of
flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262 – Codon usage bias in phylum
Actinobacteria: relevance to environmental
adaptation and host pathogenicity, 669
PCR – Expression of essential genes for
biosynthesis of antimicrobial peptides of
Bacillus is modulated by inactivated cells of
target microorganisms, 83
Penicillium oxalicum – A novel bZIP
transcription factor ClrC positively regulates
multiple stress responses, conidiation
and cellulase expression in Penicillium
oxalicum, 424
Peptidomimetics – Improved in vitro
evaluation of novel antimicrobials:
potential synergy between human plasma
and antibacterial peptidomimetics, AMPs
and antibiotics against human pathogenic
bacteria, 72
Periodontal pathogens – A dual-species
microbial model for studying the dynamics
between oral streptococci and periodontal
pathogens during biofilm development on
titanium surfaces by flow cytometry, 393
Persister – The cyclic AMP receptor protein
(CRP) regulates mqsRA, coding for the
bacterial toxin-antitoxin gene pair, in
Escherichia coli, 58
PGPR – Association of plant growth-
promoting Serratia spp. with the root
nodules of chickpea, 510
Phage regulators – Insights into aureocin
A70 regulation: participation of regulator
AurR, alternative transcription factor ␴B
and phage ␾11 regulator cI, 90
Phage replication – Propagation method for
persistent high yield of diverse Listeria
798
phages on permissive hosts at refrigeration
temperatures, 685
Phase variation – Identification and
differential production of ubiquinone-8
in the bacterial predator Bdellovibrio
bacteriovorus, 413
Phenome – Connecting phenome to genome
in Pseudomonas stutzeri 5190: an artwork
biocleaning bacterium, 757
Phenotype – Metabolic parameters linked by
phenotype microarray to acid resistance
profiles of poultryassociated Salmonella
enterica, 745
Phenotype microarray – Construction and
analysis of a genome-scale metabolic
network for Bacillus licheniformis WX-02,
282 – Phenotype MicroArray™ system
in the study of fungal functional diversity
and catabolic versatility, 710 – Use of
phenotype microarrays to study the effect
of acquisition of resistance to antimicrobials
in bacterial physiology, 723 – Phenotype
microarray analysis may unravel genetic
determinants of the stress response by
Rhodococcus aetherivorans BCP1 and
Rhodococcus opacus R7, 766 – Indole-3-
acetic acid in plant–pathogen interactions:
a key molecule for in planta bacterial
virulence and fitness, 774
Phosphotransferase system – A ptsP
deficiency in PGPR Pseudomonas
fluorescens SF39a affects bacteriocin
production and bacterial fitness in the wheat
rhizosphere, 178
Photo-acclimation – H2 production in
Rhodopseudomonas palustris as a way to
cope with high light intensities, 350
Photosynthetic quantum yield – H2
production in Rhodopseudomonas palustris
as a way to cope with high light intensities,
350
Phycomyces blakesleeanus – 51V NMR
investigation of cell-associated vanadate
species in Phycomyces blakesleeanus
mycelium, 521
Phylogenetic relationship – Fungal
communities as an experimental approach
to Darwin's naturalization hypothesis, 126
Phytopathogenic bacteria – Regulation of
pel genes, major virulence factors in the
plant pathogen bacterium Dickeya dadantii,
is mediated by cooperative binding of the
nucleoid-associated protein H-NS, 247
Pigments – Construction and phenotypic
characterization of M68, an RruI
quorum sensing knockout mutant of the
photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380
Plant growth-promoting bacteria –
Influence of tryptophan and indole-3-acetic
acid on starch accumulation in the synthetic
mutualistic Chlorella sorokiniana –
Azospirillum brasilense system under
heterotrophic conditions, 367
Keyword index / Research in Microbiology 167 (2016) 792–800
Plant growth-promoting rhizobacterium –
A ptsP deficiency in PGPR Pseudomonas
fluorescens SF39a affects bacteriocin
production and bacterial fitness in the wheat
rhizosphere, 178
Plasma – Improved in vitro evaluation of
novel antimicrobials: potential synergy
between human plasma and antibacterial
peptidomimetics, AMPs and antibiotics
against human pathogenic bacteria, 72
Plipastatin – Influence of promoters on the
production of fengycin in Bacillus spp., 272
PMA-qPCR – DVC-FISH and PMA-
qPCR techniques to assess the survival of
Helicobacter pylori inside Acanthamoeba
castellanii, 29
Poly-␥-glutamic acid – Construction and
analysis of a genome-scale metabolic
network for Bacillus licheniformis WX-02,
282
Polymerase chain reaction – A DNA tool
for early detection of vaginal dysbiosis in
African women, 133
Potentialization – Potentialization of
␤-lactams with colistin: in case of
extended spectrum ␤-lactamase producing
Escherichia coli strains isolated from
children with urinary infections, 215
Poultry – Metabolic parameters linked by
phenotype microarray to acid resistance
profiles of poultry-associated Salmonella
enterica, 745
Predator-prey interactions – Identification
and differential production of ubiquinone-8
in the bacterial predator Bdellovibrio
bacteriovorus, 413
Prodiginine biosynthesis – Sulfate as a
pivotal factor in regulation of Serratia sp.
strain S2B pigment biosynthesis, 638
Prodigiosin production optimization –
Sulfate as a pivotal factor in regulation
of Serratia sp. strain S2B pigment
biosynthesis, 638
Promoter role – Influence of promoters on
the production of fengycin in Bacillus spp.,
272
Protein structure – Characterization of newly
identified DnaA and DnaB proteins from
Acetobacter, 655
Protein – protein interaction – mutant of Escherichia coli, 462
Characterization of newly identified DnaA
and DnaB proteins from Acetobacter, 655
Proteomics – Comparative proteomics of
Acidithiobacillus ferrooxidans grown in
the presence and absence of uranium, 234
– Comparative proteomic analysis of sulfur-
oxidizing Acidithiobacillus ferrooxidans
CCM 4253 cultures having lost the ability to
couple anaerobic elemental sulfur oxidation
with ferric iron reduction, 587
Pseudomonas – A ptsP deficiency in PGPR
Pseudomonas fluorescens SF39a affects
bacteriocin production and bacterial fitness
in the wheat rhizosphere, 178 – Connecting
phenome to genome in Pseudomonas
stutzeri 5190: an artwork biocleaning
bacterium, 757
Pseudomonas protegens – A rifampicin-
resistant (rpoB) mutation in Pseudomonas
protegens Pf-5 strain leads to improved
antifungal activity and elevated production
of secondary metabolites, 625
Pseudomonas savastanoi – Indole-3-acetic
acid in plant–pathogen interactions: a key
molecule for in planta bacterial virulence
and fitness, 774
Pseudomonas syringae pv.tomato – Novel
components of leaf bacterial communities
of field-grown tomato plants and their
potential for plant growth promotion and
biocontrol of tomato diseases, 222
P-solubilization – Association of plant
growth-promoting Serratia spp. with the
root nodules of chickpea, 510
Q
Quorum sensing – Burkholderia pseudomallei
kynB plays a role in AQ production,
biofilm formation, bacterial swarming
and persistence, 159 – Construction and
phenotypic characterization of M68, an
RruI quorum sensing knockout mutant of
the photosynthetic alphaproteobacterium
Rhodospirillum rubrum, 380
R
Reaction norm – Metastable coexistence
of multiple genotypes in a constant
environment with a single resource through
fixed settings of a multiplication-survival
trade-off, 240
Reactive aldehydes – Haemophilus influenzae
strains possess variations in the global
transcriptional profile in response to oxygen
levels and this influences sensitivity to
environmental stresses, 13
Reactive oxygen species – Involvement
of the osrR gene in the hydrogen
peroxide-mediated stress response of
Corynebacterium glutamicum, 20
RecA730 protein – The Walker A motif
mutation recA4159 abolishes the SOS
response and recombination in a recA730
Regulation – Insights into aureocin A70
regulation: participation of regulator AurR,
alternative transcription factor ␴B and phage
␾11 regulator cI, 90 – A ptsP deficiency
in PGPR Pseudomonas fluorescens SF39a
affects bacteriocin production and bacterial
fitness in the wheat rhizosphere, 178
Reporter assay – Functional characterization
and transcriptome analysis reveal multiple
roles for prc in the pathogenicity of the
black rot pathogen Xanthomonas campestris
pv. campestris, 299
 Keyword index / Research in Microbiology 167 (2016) 792–800
Resource allocation – Metastable coexistence
of multiple genotypes in a constant
environment with a single resource through
fixed settings of a multiplication-survival
trade-off, 240
Respiratory chain – Efficient respiration on
TMAO requires TorD and TorE auxiliary
proteins in Shewanella oneidensis, 630
Rhodococcus – Phenotype microarray
analysis may unravel genetic determinants
of the stress response by Rhodococcus
aetherivorans BCP1 and Rhodococcus
opacus R7, 766
Rhodococcus aetherivorans BCP1 –
Phenotype microarray analysis may unravel
genetic determinants of the stress response
by Rhodococcus aetherivorans BCP1 and
Rhodococcus opacus R7, 766
Rhodococcus opacus R7 – Phenotype
microarray analysis may unravel genetic
determinants of the stress response by
Rhodococcus aetherivorans BCP1 and
Rhodococcus opacus R7, 766
Ribosome engineering – A rifampicin-
resistant (rpoB) mutation in Pseudomonas
protegens Pf-5 strain leads to improved
antifungal activity and elevated production
of secondary metabolites, 625
Rifampicin resistance – A rifampicin-
resistant (rpoB) mutation in Pseudomonas
protegens Pf-5 strain leads to improved
antifungal activity and elevated production
of secondary metabolites, 625
Río Tinto – Lessons learned from thirty years
of geomicrobiological studies of Río Tinto,
539
RNA seq – Iron deficiency resistance
mechanisms enlightened by gene expression
analysis in Paenibacillus riograndensis
SBR5, 501
RpoS sigma factor – Metastable coexistence
of multiple genotypes in a constant
environment with a single resource through
fixed settings of a multiplication-survival
trade-off, 240
RT-qPCR – Are there multiple mechanisms
of anaerobic sulfur oxidation with ferric
iron in Acidithiobacillus ferrooxidans?, 357
– Iron deficiency resistance mechanisms
enlightened by gene expression analysis in
Paenibacillus riograndensis SBR5, 501
S factor ␴B and phage ␾11 regulator cI, 90
Safety – Connecting phenome to genome in
Pseudomonas stutzeri 5190: an artwork
biocleaning bacterium, 757
Salmonella – Metabolic parameters linked
by phenotype microarray to acid resistance
profiles of poultry-associated Salmonella
enterica, 745
Sea surface microlayer – Diversity of yeasts
associated with the sea surface microlayer
and underlying water along the northern
coast of Taiwan, 35
Secondary metabolite – Antimicrobial
compounds from endophytic Streptomyces
sp. BCC72023 isolated from rice (Oryza
sativa L.), 290 – A rifampicin-resistant
(rpoB) mutation in Pseudomonas protegens
Pf-5 strain leads to improved antifungal
activity and elevated production of
secondary metabolites, 625
Septal localization – Septal localization
by membrane targeting sequences and a
conserved sequence essential for activity
at the COOH-terminus of Bacillus subtilis
cardiolipin synthase, 202
Serratia marcescens – Sulfate as a pivotal
factor in regulation of Serratia sp. strain
S2B pigment biosynthesis, 638
Serratia spp. – Association of plant growth-
promoting Serratia spp. with the root
nodules of chickpea, 510
␴B – Insights into aureocin A70 regulation:
participation of regulator AurR, alternative
transcription factor ␴B and phage ␾11
regulator cI, 90
Signal processing – Phase-dependent
dynamics of the lac promoter under nutrient
stress, 451
Single-cell analysis – Phase-dependent
dynamics of the lac promoter under nutrient
stress, 451
Soil – Occurrence of Stenotrophomonas
maltophilia in agricultural soils and
antibiotic resistance properties, 313 –
Metagenomes provide valuable comparative
information on soil microeukaryotes, 436
Solanum lycopersicum – Detection of
biosynthetic gene and phytohormone
production by endophytic actinobacteria
associated with Solanum lycopersicum and
their plant-growth-promoting effect, 692
Sphingosine bases – The antimicrobial
potential of algicolous marine fungi for
counteracting multidrug-resistant bacteria:
phylogenetic diversity and chemical
profiling, 492
Sporulation – A single amino acid mutation
in Spo0A results in sporulation deficiency
of Paenibacillus polymyxa SC2, 472
Staphylococcus aureus – Insights into
aureocin A70 regulation: participation of
regulator AurR, alternative transcription
Stenotrophomonas maltophilia – Occurrence
of Stenotrophomonas maltophilia in
agricultural soils and antibiotic resistance
properties, 313
Streptococcus equi ssp. zooepidemicus –
The arginine deiminase system facilitates
environmental adaptability of Streptococcus
equi ssp. zooepidemicus through pH
adjustment, 403
Streptomyces – Antimicrobial compounds
799
from endophytic Streptomyces sp.
BCC72023 isolated from rice (Oryza sativa
L.), 290
Stress – Comparative proteomics of
Acidithiobacillus ferrooxidans grown in the
presence and absence of uranium, 234
Stress resistance – Metastable coexistence
of multiple genotypes in a constant
environment with a single resource through
fixed settings of a multiplication-survival
trade-off, 240
Stress response – Haemophilus influenzae
strains possess variations in the global
transcriptional profile in response to oxygen
levels and this influences sensitivity to
environmental stresses, 13 – Alternative
scenarios of starvation-induced adaptation
in Pectobacterium atrosepticum, 254 –
Phenotype microarray analysis may unravel
genetic determinants of the stress response
by Rhodococcus aetherivorans BCP1 and
Rhodococcus opacus R7, 766
Substrate utilisation – Phenotype
MicroArray™ system in the study of fungal
functional diversity and catabolic versatility,
710
Sulfate effect – Sulfate as a pivotal factor
in regulation of Serratia sp. strain S2B
pigment biosynthesis, 638
Sulfolobus – Saline-water bioleaching of
chalcopyrite with thermophilic, iron(II)-
and sulfur-oxidizing microorganisms, 546
– Microbial community profiling of the
Chinoike Jigoku (“Blood Pond Hell”)
hot spring in Beppu, Japan: isolation
and characterization of Fe(III)-reducing
Sulfolobus sp. strain GA1, 595
Sulfolobus metallicus – Biofilm formation and
interspecies interactions in mixed cultures
of thermo-acidophilic archaea Acidianus
spp. and Sulfolobus metallicus, 604
Sulfur metabolism – Are there multiple
mechanisms of anaerobic sulfur oxidation
with ferric iron in Acidithiobacillus
ferrooxidans?, 357 – Comparative
proteomic analysis of sulfur-oxidizing
Acidithiobacillus ferrooxidans CCM 4253
cultures having lost the ability to couple
anaerobic elemental sulfur oxidation with
ferric iron reduction, 587
Swimming motility – RpoS differentially
affects the general stress response and
biofilm formation in the endophytic Serratia
plymuthica G3, 168
Synergistic action – Improved in vitro evaluation
of novel antimicrobials: potential synergy
between human plasma and antibacterial
peptidomimetics, AMPs and antibiotics
against human pathogenic bacteria, 72
– Significant antibacterial activity and
synergistic effects of camel lactoferrin with
antibiotics against methicillin-resistant
Staphylococcus aureus (MRSA), 480
Synthetic mutualism – Influence of
tryptophan and indole-3-acetic acid
800
on starch accumulation in the synthetic
mutualistic Chlorella sorokiniana –
Azospirillum brasilense system under
heterotrophic conditions, 367
T Transcriptome sequencing – A single
Thermoacidophiles – Saline-water
bioleaching of chalcopyrite with
thermophilic, iron(II)- and sulfur-oxidizing
microorganisms, 546
Thermo-acidophilic archaea – Biofilm
formation and interspecies interactions
in mixed cultures of thermo-acidophilic
archaea Acidianus spp. and Sulfolobus
metallicus, 604
Titanium – A dual-species microbial model
for studying the dynamics between oral
streptococci and periodontal pathogens
during biofilm development on titanium
surfaces by flow cytometry, 393
TMAO respiration – Efficient respiration on
TMAO requires TorD and TorE auxiliary
proteins in Shewanella oneidensis, 630
Toxic compounds – Phenotype microarray
analysis may unravel genetic determinants
of the stress response by Rhodococcus
aetherivorans BCP1 and Rhodococcus
opacus R7, 766
Toxin – The cyclic AMP receptor protein
(CRP) regulates mqsRA, coding for the
bacterial toxin-antitoxin gene pair, in
Escherichia coli, 58
Trade-offs – Metastable coexistence
of multiple genotypes in a constant
environment with a single resource through
fixed settings of a multiplication-survival
trade-off, 240
Transcription factor – A novel bZIP
transcription factor ClrC positively regulates
multiple stress responses, conidiation
and cellulase expression in Penicillium
oxalicum, 424
Transcriptional regulation – Functional
characterization and transcriptome
Keyword index / Research in Microbiology 167 (2016) 792–800
analysis reveal multiple roles for prc in
the pathogenicity of the black rot pathogen
Xanthomonas campestris pv. campestris,
299
amino acid mutation in Spo0A results in
sporulation deficiency of Paenibacillus
polymyxa SC2, 472
Trichoderma cf. harzianum – Fungal
communities as an experimental approach
to Darwin's naturalization hypothesis, 126
Tryptophan – Influence of tryptophan and
indole-3-acetic acid on starch accumulation
in the synthetic mutualistic Chlorella
sorokiniana – Azospirillum brasilense
system under heterotrophic conditions, 367
Type three secretion system – Indole-3-acetic
acid in plant–pathogen interactions: a key
molecule for in planta bacterial virulence
and fitness, 774
Typing – Detection, identification and typing
of Acidithiobacillus species and strains: a
review, 555
U W
Uncultivable microorganisms – Separating
and characterizing functional alkane
degraders from crude-oil-contaminated
sites via magnetic nanoparticle-mediated
isolation, 731
Underlying water – Diversity of yeasts
associated with the sea surface microlayer
and underlying water along the northern
coast of Taiwan, 35
UPLC-ESI-MS/MS – Detection of
biosynthetic gene and phytohormone
production by endophytic actinobacteria
associated with Solanum lycopersicum and
their plant-growth-promoting effect, 692
Uranium resistance – Comparative proteomics
of Acidithiobacillus ferrooxidans grown in
the presence and absence of uranium, 234
V
51V
Vanadate – NMR investigation of cell-
associated vanadate species in Phycomyces
blakesleeanus mycelium, 521
Viable but non-culturable cells – Alternative
scenarios of starvation-induced adaptation
in Pectobacterium atrosepticum, 254
Virulence – Elucidation of the functional role
of flagella in virulence and ecological traits
of Pseudomonas cichorii using flagella
absence (⌬fliJ) and deficiency (⌬fliI)
mutants, 262 – Functional characterization
and transcriptome analysis reveal multiple
roles for prc in the pathogenicity of the
black rot pathogen Xanthomonas campestris
pv. campestris, 299
Virulence factors – Burkholderia
pseudomallei kynB plays a role in AQ
production, biofilm formation, bacterial
swarming and persistence, 159
Virulence gene – Genetic diversity, the
virulence gene profile and antimicrobial
resistance of clinical mastitis-associated
Escherichia coli, 678
Wastewater – Electricity generation from
an inorganic sulfur compound containing
mining wastewater by acidophilic
microorganisms, 568
Water springs – Spatial and temporal
variability of bacterial communities in high
alpine water spring sediments, 325
Y
Yeast community – Diversity of yeasts
associated with the sea surface microlayer
and underlying water along the northern
coast of Taiwan, 35
Yersinia enterocolitica – Propagation method
for persistent high yield of diverse Listeria
phages on permissive hosts at refrigeration
temperatures, 685