bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and Structure of Bacterial Chemolithotrophic Communities in Pine Forest and Agroecosystem Soils
Authors: Tolli J. , King G. M. 
Published: December 2005

ABSTRACT

Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (>50 years old). The extracts have been used in PCR amplifications of the
cbbL
gene for the rubisCO large subunit protein.
cbbL
PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing
Nitrosospira
. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.
New Multiple-Deletion Method for the
Corynebacterium glutamicum
Genome, Using a Mutant
lox
Sequence
Authors: Suzuki Nobuaki , Nonaka Hiroshi , Tsuge Yota , Inui Masayuki , Yukawa Hideaki 
Published: December 2005

ABSTRACT

Due to the difficulty of multiple deletions using the Cre/
loxP
system, a simple, markerless multiple-deletion method based on a Cre
/
mutant
lox
system combining a right-element (RE) mutant
lox
site with a left-element (LE) mutant
lox
site was employed for large-scale genome rearrangements in
Corynebacterium glutamicum
. Eight distinct genomic regions that had been identified previously by comparative analysis of
C. glutamicum
R and
C. glutamicum
13032 genomes were targeted for deletion. By homologous recombination, LE and RE mutant
lox
sites were integrated at each end of a target region. Highly efficient and accurate deletions between the two chromosomal mutant
lox
sites in the presence of Cre recombinase were realized. A deletion mutant lacking 190 kb of chromosomal regions, encoding a total of 188 open reading frames (ORFs), was obtained. These deletions represent the largest genomic excisions in
C. glutamicum
reported to date. Despite the loss of numerous predicted ORFs, the mutant exhibited normal growth under standard laboratory conditions. The Cre/
loxP
system using a pair of mutant
lox
sites provides a new, efficient genome rearrangement technique for
C. glutamicum
. It should facilitate the understanding of genome functions of microorganisms.
Development of a Rapid Assay for Determining the Relative Abundance of Bacteria
Authors: Rowan Arlene K. , Davenport Russell J. , Snape Jason R. , Fearnside David , Barer Michael R. , Curtis Thomas P. , Head Ian M. 
Published: December 2005

ABSTRACTA sandwich hybridization assay for high-throughput, rapid, simple, and inexpensive quantification of specific microbial populations was evaluated. The assay is based on the hybridization of a target rRNA with differentially labeled capture and detector probes. Betaproteobacterial ammonia-oxidizing bacteria (AOB) were selected as the target group for the study, since they represent a phylogenetically coherent group of organisms that perform a well-defined geochemical function in natural and engineered environments. Reagent concentrations, probe combinations, and washing, blocking, and hybridization conditions were optimized to improve signal and reduce background. The detection limits for the optimized RNA assay were equivalent to approximately 103to 104and 104to 105bacterial cells, respectively, forE. colirRNA and RNA extracted from activated sludge, by using probes targeting the majority of bacteria. Furthermore, the RNA assay had good specificity, permitted discrimination of rRNA sequences that differed by a 2-bp mismatch in the probe target region, and could distinguish the sizes of AOB populations in nitrifying and nonnitrifying wastewater treatment plants.
Horizontal Gene Transfer to Endogenous Endophytic Bacteria from Poplar Improves Phytoremediation of Toluene
Authors: Taghavi Safiyh , Barac Tanja , Greenberg Bill , Borremans Brigitte , Vangronsveld Jaco , van der Lelie Daniel 
Published: December 2005

ABSTRACT

Poplar, a plant species frequently used for phytoremediation of groundwater contaminated with organic solvents, was inoculated with the endophyte
Burkholderia cepacia
VM1468. This strain, whose natural host is yellow lupine, contains the pTOM-Bu61 plasmid coding for constitutively expressed toluene degradation. Noninoculated plants or plants inoculated with the soil bacterium
B. cepacia
Bu61(pTOM-Bu61) were used as controls. Inoculation of poplar had a positive effect on plant growth in the presence of toluene and reduced the amount of toluene released via evapotranspiration. These effects were more dramatic for VM1468, the endophytic strain, than for Bu61. Remarkably, none of the strains became established at detectable levels in the endophytic community, but there was horizontal gene transfer of pTOM-Bu61 to different members of the endogenous endophytic community, both in the presence and in the absence of toluene. This work is the first report of in planta horizontal gene transfer among plant-associated endophytic bacteria and demonstrates that such transfer could be used to change natural endophytic microbial communities in order to improve the remediation of environmental insults.
Effects of Aeration Cycles on Nitrifying Bacterial Populations and Nitrogen Removal in Intermittently Aerated Reactors
Authors: Mota Cesar , Head Melanie A. , Ridenoure Jennifer A. , Cheng Jay J. , de los Reyes Francis L. 
Published: December 2005

ABSTRACT

The effects of the lengths of aeration and nonaeration periods on nitrogen removal and the nitrifying bacterial community structure were assessed in intermittently aerated (IA) reactors treating digested swine wastewater. Five IA reactors were operated in parallel with different aeration-to-nonaeration time ratios (ANA). Populations of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were monitored using 16S rRNA slot blot hybridizations. AOB species diversity was assessed using
amoA
gene denaturant gradient gel electrophoresis.
Nitrosomonas
and
Nitrosococcus mobilis
were the dominant AOB and
Nitrospira
spp. were the dominant NOB in all reactors, although
Nitrosospira
and
Nitrobacter
were also detected at lower levels. Reactors operated with the shortest aeration time (30 min) showed the highest
Nitrosospira
rRNA levels, and reactors operated with the longest anoxic periods (3 and 4 h) showed the lowest levels of
Nitrobacter
, compared to the other reactors.
Nitrosomonas
sp. strain Nm107 was detected in all reactors, regardless of the reactor's performance. Close relatives of
Nitrosomonas europaea
,
Nitrosomonas
sp. strain ENI-11, and
Nitrosospira multiformis
were occasionally detected in all reactors. Biomass fractions of AOB and effluent ammonia concentrations were not significantly different among the reactors. NOB were more sensitive than AOB to long nonaeration periods, as nitrite accumulation and lower total NOB rRNA levels were observed for an ANA of 1 h:4 h. The reactor with the longest nonaeration time of 4 h performed partial nitrification, followed by denitrification via nitrite, whereas the other reactors removed nitrogen through traditional nitrification and denitrification via nitrate. Superior ammonia removal efficiencies were not associated with levels of specific AOB species or with higher AOB species diversity.
Effect of Iron on Growth and Ultrastructure of
Acaryochloris marina
Authors: Swingley Wesley D. , Hohmann-Marriott Martin F. , Le Olson Tien , Blankenship Robert E. 
Published: December 2005

ABSTRACT

The cyanobacterial genus
Acaryochloris
is the only known group of oxygenic phototrophs that contain chlorophyll
d
rather than chlorophyll
a
as the major photosynthetic pigment. Studies on this organism are still in their earliest stages, and biochemical analysis has rapidly outpaced growth optimization. We have investigated culture growth of the major strains of
Acaryochloris marina
(MBIC11017 and MBIC10697) by using several published and some newly developed growth media. It was determined that heavy addition of iron significantly enhanced culture longevity. These high-iron cultures showed an ultrastructure with thylakoid stacks that resemble traditional cyanobacteria (unlike previous studies). These cultures also show a novel reversal in the pigment ratios of the photosystem II signature components chlorophyll
a
and pheophytin
a
, as opposed to those in previous studies.
Interactions between the Fe(III)-Reducing Bacterium
Geobacter sulfurreducens
and Arsenate, and Capture of the Metalloid by Biogenic Fe(II)
Authors: Islam F. S. , Pederick R. L. , Gault A. G. , Adams L. K. , Polya D. A. , Charnock J. M. , Lloyd J. R. 
Published: December 2005

ABSTRACT

Previous work has shown that microbial communities in As-mobilizing sediments from West Bengal were dominated by
Geobacter
species. Thus, the potential of
Geobacter sulfurreducens
to mobilize arsenic via direct enzymatic reduction and indirect mechanisms linked to Fe(III) reduction was analyzed.
G. sulfurreducens
was unable to conserve energy for growth via the dissimilatory reduction of As(V), although it was able to grow in medium containing fumarate as the terminal electron acceptor in the presence of 500 μM As(V). There was also no evidence of As(III) in culture supernatants, suggesting that resistance to 500 μM As(V) was not mediated by a classical arsenic resistance operon, which would rely on the intracellular reduction of As(V) and the efflux of As(III). When the cells were grown using soluble Fe(III) as an electron acceptor in the presence of As(V), the Fe(II)-bearing mineral vivianite was formed. This was accompanied by the removal of As, predominantly as As(V), from solution. Biogenic siderite (ferrous carbonate) was also able to remove As from solution. When the organism was grown using insoluble ferrihydrite as an electron acceptor, Fe(III) reduction resulted in the formation of magnetite, again accompanied by the nearly quantitative sorption of As(V). These results demonstrate that
G. sulfurreducens
, a model Fe(III)-reducing bacterium, did not reduce As(V) enzymatically, despite the apparent genetic potential to mediate this transformation. However, the reduction of Fe(III) led to the formation of Fe(II)-bearing phases that are able to capture arsenic species and could act as sinks for arsenic in sediments.
Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and Xylene Compounds by
Dechloromonas
Strain RCB
Authors: Chakraborty Romy , O'Connor Susan M. , Chan Emily , Coates John D. 
Published: December 2005

ABSTRACT

Dechloromonas
strain RCB has been shown to be capable of anaerobic degradation of benzene coupled to nitrate reduction. As a continuation of these studies, the metabolic versatility and hydrocarbon biodegradative capability of this organism were investigated. The results of these revealed that in addition to nitrate, strain RCB could alternatively degrade benzene both aerobically and anaerobically with perchlorate or chlorate [(per)chlorate] as a suitable electron acceptor. Furthermore, with nitrate as the electron acceptor, strain RCB could also utilize toluene, ethylbenzene, and all three isomers of xylene (
ortho
-,
meta
-, and
para
-) as electron donors. While toluene and ethylbenzene were completely mineralized to CO
2
, strain RCB did not completely mineralize
para
-xylene but rather transformed it to some as-yet-unidentified metabolite. Interestingly, with nitrate as the electron acceptor, strain RCB degraded benzene and toluene concurrently when the hydrocarbons were added as a mixture and almost 92 μM total hydrocarbons were oxidized within 15 days. The results of these studies emphasize the unique metabolic versatility of this organism, highlighting its potential applicability to bioremediative technologies.
Effects of Growth in the Presence of Subinhibitory Concentrations of Dicloxacillin on
Staphylococcus epidermidis
and
Staphylococcus haemolyticus
Biofilms
Authors: Cerca Nuno , Martins Silvia , Sillankorva Sanna , Jefferson Kimberly K. , Pier Gerald B. , Oliveira Rosario , Azeredo Joana 
Published: December 2005

ABSTRACT

Low concentrations of antibiotics can inhibit microbial adherence to medical device surfaces. However, little is known about the changes that occur in the physiology of bacteria within biofilms formed in the presence of subinhibitory (sub-MIC) concentrations of antibiotics. In this study, the densities and matrix compositions ofbiofilms formed by two coagulase-negative
Staphylococcus
species in the absence and in the presence of sub-MIC concentrations of dicloxacillin were evaluated. Biofilms formed in the presence of sub-MIC concentrations of dicloxacillin contained less biomass, and there were notable changes in the composition of the biofilm matrix. Changes in the spatial structure were also verified by confocal scanning laser microscopy, indicating that biofilms grown in the presence of sub-MIC concentrations of dicloxicilln had a lower cell density. Physiological alterations in the bacteria within biofilms grown in the presence of subinhibitory concentrations of the antibiotic were also evaluated. The results showed that there were differences in bacterial surface characteristics when cultures were grown in the presence of sub-MIC concentrations of dicloxacillin, including decreased hydrophobicity and decreased expression of the exopolysaccharide poly-
N
-acetylglucosamine. The elemental composition of the cell surface was also analyzed, and whereas in
Staphylococcus epidermidis
there were decreases in the oxygen and nitrogen contents, in
Staphylococcus haemolyticus
there were increases in these two parameters. Additionally, increases in resistance to several antibiotics were observed for the cells within biofilms formed in the presence of dicloxacillin.
Investigation of an Acetate-Fed Denitrifying Microbial Community by Stable Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescent In Situ Hybridization-Microautoradiography
Authors: Ginige Maneesha P. , Keller Jürg , Blackall Linda L. 
Published: December 2005

ABSTRACT

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [
13
C]acetate was used in SIP to label the DNA of the denitrifiers. The [
13
C]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the
13
C library were closely related to the bacterial families
Comamonadaceae
and
Rhodocyclaceae
in the class
Betaproteobacteria
. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking up [
14
C]acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the wastewater industry to enhance denitrification.
Application of Stereolithographic Custom Models for Studying the Impact of Biofilms and Mineral Precipitation on Fluid Flow
Authors: Stoner D. L. , Watson S. M. , Stedtfeld R. D. , Meakin P. , Griffel L. K. , Tyler T. L. , Pegram L. M. , Barnes J. M. , Deason V. A. 
Published: December 2005

ABSTRACTHere we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. The internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. High-resolution digital time-lapse imaging was employed to qualitatively observe the migration of colloidal and soluble dyes through the flow models. In this study, aSphingomonassp. andSporosarcina (Bacillus) pasteuriiinfluenced the fluid dynamics by physically altering flow paths. Microbial colonization and calcite deposition enhanced the stagnant regions adjacent to solid boundaries. Microbial growth and calcite precipitation occurred to a greater extent in areas behind the fabricated obstacles and less in high-velocity orifices.
Desulfotomaculum
and
Methanobacterium
spp. Dominate a 4- to 5-Kilometer-Deep Fault
Authors: Moser Duane P. , Gihring Thomas M. , Brockman Fred J. , Fredrickson James K. , Balkwill David L. , Dollhopf Michael E. , Lollar Barbara Sherwood , Pratt Lisa M. , Boice Erik , Southam Gordon , Wanger Greg , Baker Brett J. , Pfiffner Susan M. , Lin Li-Hung , Onstott T. C. 
Published: December 2005

ABSTRACT

Alkaline, sulfidic, 54 to 60°C, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures >3.3 km beneath the surface supported a microbial community dominated by a bacterial species affiliated with
Desulfotomaculum
spp. and an archaeal species related to
Methanobacterium
spp. The geochemical homogeneity over the 650-m length of the borehole, the lack of dividing cells, and the absence of these microorganisms in mine service water support an indigenous origin for the microbial community. The coexistence of these two microorganisms is consistent with a limiting flux of inorganic carbon and SO
4
2−
in the presence of high pH, high concentrations of H
2
and CH
4
, and minimal free energy for autotrophic methanogenesis. Sulfide isotopic compositions were highly enriched, consistent with microbial SO
4
2−
reduction under hydrologic isolation. An analogous microbial couple and similar abiogenic gas chemistry have been reported recently for hydrothermal carbonate vents of the Lost City near the Mid-Atlantic Ridge (D. S. Kelly et al., Science
307:
1428-1434, 2005), suggesting that these features may be common to deep subsurface habitats (continental and marine) bearing this geochemical signature. The geochemical setting and microbial communities described here are notably different from microbial ecosystems reported for shallower continental subsurface environments.
Engineering
Pseudomonas fluorescens
for Biodegradation of 2,4-Dinitrotoluene
Authors: Monti Mariela R. , Smania Andrea M. , Fabro Georgina , Alvarez María E. , Argaraña Carlos E. 
Published: December 2005

ABSTRACT

Using the genes encoding the 2,4-dinitrotoluene degradation pathway enzymes, the nonpathogenic psychrotolerant rhizobacterium
Pseudomonas fluorescens
ATCC 17400 was genetically modified for degradation of this priority pollutant. First, a recombinant strain designated MP was constructed by conjugative transfer from
Burkholderia
sp. strain DNT of the pJS1 megaplasmid, which contains the
dnt
genes for 2,4-dinitrotoluene degradation. This strain was able to grow on 2,4-dinitrotoluene as the sole source of carbon, nitrogen, and energy at levels equivalent to those of
Burkholderia
sp. strain DNT. Nevertheless, loss of the 2,4-dinitrotoluene degradative phenotype was observed for strains carrying pJS1. The introduction of
dnt
genes into the
P.fluorescens
ATCC 17400 chromosome, using a suicide chromosomal integration Tn
5
-based delivery plasmid system, generated a degrading strain that was stable for a long time, which was designated RE. This strain was able to use 2,4-dinitrotoluene as a sole nitrogen source and to completely degrade this compound as a cosubstrate. Furthermore,
P. fluorescens
RE, but not
Burkholderia
sp. strain DNT, was capable of degrading 2,4-dinitrotoluene at temperatures as low as 10°C. Finally, the presence of
P. fluorescens
RE in soils containing levels of 2,4-dinitrotoluene lethal to plants significantly decreased the toxic effects of this nitro compound on
Arabidopsis thaliana
growth. Using synthetic medium culture,
P. fluorescens
RE was found to be nontoxic for
A.thaliana
and
Nicotiana tabacum
, whereas under these conditions
Burkholderia
sp. strain DNT inhibited
A.thaliana
seed germination and was lethal to plants. These features reinforce the advantageous environmental robustness of
P. fluorescens
RE compared with
Burkholderia
sp. strain DNT.
Structural Characterization of Glucooligosaccharide Oxidase from
Acremonium strictum
Authors: Lee Meng-Hwan , Lai Wen-Lin , Lin Shuen-Fuh , Hsu Cheng-Sheng , Liaw Shwu-Huey , Tsai Ying-Chieh 
Published: December 2005

ABSTRACT

Glucooligosaccharide oxidase from
Acremonium strictum
was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in
Pichia pastoris
, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the

K
m

. Instead, the variants displayed
k
cat
values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin.