bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid
Anomoneura mori
(Insecta, Homoptera)
Authors: Fukatsu Takema , Nikoh Naruo 
Published: December 2019

ABSTRACT

We characterized the intracellular symbiotic bacteria of the mulberry psyllid
Anomoneura mori
by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA of
A. mori
, and two clones, the A-type and B-type clones, were identified by restriction fragment length polymorphism analysis. In situ hybridization with specific oligonucleotide probes demonstrated that the A-type and B-type 16S rDNAs were derived from the X-symbionts and Y-symbionts, respectively. Molecular phylogenetic analyses of the 16S rDNA sequences showed that these symbionts belong to distinct lineages in the γ subdivision of the
Proteobacteria
. No 16S rDNA sequences in the databases were closely related to the 16S rDNA sequences of the X- and Y-symbionts. However, the sequences that were relatively closely related to them were the sequences of endosymbionts of other insects. The nucleotide compositions of the 16S rDNAs of the X- and Y-symbionts were highly AT biased, and the sequence of the X-symbiont was the most AT-rich bacterial 16S rDNA sequence reported so far.
Plasmids Responsible for Horizontal Transfer of Naphthalene Catabolism Genes between Bacteria at a Coal Tar-Contaminated Site Are Homologous to pDTG1 from
Pseudomonas putida
NCIB 9816-4
Authors: Stuart-Keil K. G. , Hohnstock A. M. , Drees K. P. , Herrick J. B. , Madsen E. L. 
Published: December 2019

ABSTRACT

The presence of a highly conserved
nahAc
allele among phylogenetically diverse bacteria carrying naphthalene-catabolic plasmids provided evidence for in situ horizontal gene transfer at a coal tar-contaminated site (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330–2337, 1997). The objective of the present study was to identify and characterize the different-sized naphthalene-catabolic plasmids in order to determine the probable mechanism of horizontal transfer of the
nahAc
gene in situ. Filter matings between naphthalene-degrading bacterial isolates and their cured progeny revealed that the naphthalene-catabolic plasmids were self-transmissible. Limited interstrain transfer was also found. Analysis of the restriction fragment length polymorphism (RFLP) patterns indicated that catabolic plasmids from 12 site-derived isolates were closely related to each other and to the naphthalene-catabolic plasmid (pDTG1) of
Pseudomonas putida
NCIB 9816-4, which was isolated decades ago in Bangor, Wales. The similarity among all site-derived naphthalene-catabolic plasmids and pDTG1 was confirmed by using the entire pDTG1 plasmid as a probe in Southern hybridizations. Two distinct but similar naphthalene-catabolic plasmids were retrieved directly from the microbial community indigenous to the contaminated site in a filter mating by using a cured, rifampin-resistant site-derived isolate as the recipient. RFLP patterns and Southern hybridization showed that both of these newly retrieved plasmids, like the isolate-derived plasmids, were closely related to pDTG1. These data indicate that a pDTG1-like plasmid is the mobile genetic element responsible for transferring naphthalene-catabolic genes among bacteria in situ. The pervasiveness and persistence of this naphthalene-catabolic plasmid suggest that it may have played a role in the adaptation of this microbial community to the coal tar contamination at our study site.
A Plant Growth-Promoting Bacterium That Decreases Nickel Toxicity in Seedlings
Authors: Burd Genrich I. , Dixon D. George , Glick Bernard R. 
Published: December 2019

ABSTRACTA plant growth-promoting bacterium,Kluyvera ascorbataSUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni2+, Pb2+, Zn2+, and CrO4−, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence ofK. ascorbataSUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.
Characterization of
aflJ
, a Gene Required for Conversion of Pathway Intermediates to Aflatoxin
Authors: Meyers D. M. , Obrian G. , Du W. L. , Bhatnagar D. , Payne G. A. 
Published: December 2019

ABSTRACT

The genes encoding the aflatoxin biosynthetic pathway enzymes have been localized as a cluster to a 75-kb DNA fragment. The enzymatic functions of the products of most of the genes in the cluster are known, but there are a few genes that have not yet been characterized. We report here the characterization of one of these genes, a gene designated
aflJ
. This gene resides in the cluster adjacent to the pathway regulatory gene,
aflR
, and the two genes are divergently transcribed. Disruption of
aflJ
in
Aspergillus flavus
results in a failure to produce aflatoxins and a failure to convert exogenously added pathway intermediates norsolorinic acid, sterigmatocystin, and
O
-methylsterigmatocystin to aflatoxin. The disrupted strain does, however, accumulate
pksA
,
nor-1
,
ver-1
, and
omtA
transcripts under conditions conducive to aflatoxin biosynthesis. Therefore, disruption of
aflJ
does not affect transcription of these genes, and
aflJ
does not appear to have a regulatory function similar to that of
aflR
. Sequence analysis of
aflJ
and its putative peptide, AflJ, did not reveal any enzymatic domains or significant similarities to proteins of known function. The putative peptide does contain three regions predicted to be membrane-spanning domains and a microbodies C-terminal targeting signal.
Distribution and Life Strategies of Two Bacterial Populations in a Eutrophic Lake
Authors: Weinbauer Markus G. , Höfle Manfred G. 
Published: December 2019

ABSTRACT

Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plußsee and characterize their life strategies. Populations of
Comamonas acidovorans
PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas
Aeromonas hydrophila
PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i.e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h
−1
) were higher than those of the entire bacterial community (0.04 to 0.08 h
−1
) but lower than those of PU7718 (0.26 to 0.31 h
−1
). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically versatile
A. hydrophila
PU7718 is an
r
-strategist or opportunistic population in Lake Plußsee, whereas the grazing-resistant
C. acidovorans
PX54 is rather a
K
-strategist or equilibrium population.
Degradation of 1,2,3,4-Tetrachlorobenzene by
Pseudomonas chlororaphis
RW71
Authors: Potrawfke Thomas , Timmis Kenneth Nigel , Wittich Rolf-Michael 
Published: December 2019

ABSTRACT

Pseudomonas chlororaphis
RW71 mineralized 1,2,3,4-tetrachlorobenzene, a highly recalcitrant pollutant hitherto not known to be degraded by pure cultures, as a sole source of carbon and energy, thereby releasing stoichiometric amounts of chloride. The transient excretion of tetrachlorocatechol in the early growth phase suggests an initial attack by a dioxygenase to form the corresponding dihydrodiol which rearomatizes to the catechol. The activity of chlorocatechol 1,2-dioxygenase in crude cell extracts was found to be extraordinarily high towards 3-chlorocatechol (ratio of 2.6 compared to catechol) and other chlorocatechols, including tetrachlorocatechol, which was transformed at a low but significant rate. Further identification of tetrachloromuconic acid, 2,3,5-trichlorodienelactone, 2,3,5-trichloromaleyl acetic acid, and 2,4-dichloro-3-oxoadipic acid as their methyl esters, together with high specific enzyme activities for chlorinated substrates, implicated a functioning chlorocatechol pathway to be induced during growth.
New Hybrids betweenSaccharomycesSensu Stricto Yeast Species Found among Wine and Cider Production Strains
Authors: Masneuf Isabelle , Hansen Jørgen , Groth Casper , Piskur Jure , Dubourdieu Denis 
Published: December 2019

ABSTRACTTwo yeast isolates, a wine-making yeast first identified as a Mel+strain (ex.S. uvarum) and a cider-making yeast, were characterized for their nuclear and mitochondrial genomes. Electrophoretic karyotyping analyses, restriction fragment length polymorphism maps of PCR-amplifiedMET2gene fragments, and the sequence analysis of a part of the twoMET2gene alleles found support the notion that these two strains constitute hybrids betweenSaccharomyces cerevisiaeandSaccharomyces bayanus. The two hybrid strains had completely different restriction patterns of mitochondrial DNA as well as different sequences of theOLI1gene. The sequence of theOLI1gene from the wine hybrid strain appeared to be the same as that of theS. cerevisiaegene, whereas theOLI1gene of the cider hybrid strain is equally divergent from both putative parents,S. bayanusandS. cerevisiae. Some fermentative properties were also examined, and one phenotype was found to reflect the hybrid nature of these two strains. The origin and nature of such hybridization events are discussed.
Effects of Visible Light and UV Radiation on Photosynthesis in a Population of a Hot Spring Cyanobacterium, a
Synechococcus
sp., Subjected to High-Temperature Stress
Authors: Miller Scott R. , Wingard Christopher E. , Castenholz Richard W. 
Published: December 2019

ABSTRACT

Assays of photosynthesis were conducted with a biofilm population of a cyanobacterium, a
Synechococcus
sp., growing at ∼70°C in a Yellowstone National Park hot spring to test whether cells growing near the upper temperature limit of photosynthetic life are optimally adapted to their mean environmental temperature. Cell suspensions were assayed at 70, 65, and 55°C while being simultaneously exposed to modified solar environments, including reduction of total irradiance and exclusion of UV radiation. Carbon fixation was greatest at 65°C, while 70 and 55°C were always supraoptimal and suboptimal for photosynthesis, respectively. The degree of temperature stress was dependent upon light intensity, and this light-dependent temperature effect may involve both reduced quantum efficiency at subsaturating irradiances and a lower saturating irradiance at both supraoptimal and suboptimal temperatures. The
Synechococcus
sp. was also more susceptible to UV inhibition of photosynthesis at nonoptimal temperatures. These results suggest that this population is persisting at a nearly lethal temperature and is consequently subject to greater damage by both visible and UV radiation, but it is speculated that these cells may be avoiding competition with other photoautotrophs under these nonoptimal conditions. In separate experiments monitoring diurnal patterns of photosynthesis, cells exhibited peak productivity during the morning, followed by an afternoon decline. No recovery of photosynthesis was observed during the remaining daytime, and carbon fixation was always UV inhibited under conditions of photosynthetically saturating light.
Determination of the Biomasses of Small Bacteria at Low Concentrations in a Mixture of Species with Forward Light Scatter Measurements by Flow Cytometry
Authors: Robertson B. R. , Button D. K. , Koch A. L. 
Published: December 2019

ABSTRACT

The forward light scatter intensity of bacteria analyzed by flow cytometry varied with their dry mass, in accordance with theory. A standard curve was formulated with Rayleigh-Gans theory to accommodate cell shape and alignment. It was calibrated with an extinction-culture isolate of the small marine organism
Cycloclasticus oligotrophus
, for which dry weight was determined by CHN analysis and
14
C-acetate incorporation. Increased light scatter intensity due to formaldehyde accumulation in preserved cells was included in the standard curve. When differences in the refractive indices of culture media and interspecies differences in the effects of preservation were taken into account, there was agreement between cell mass obtained by flow cytometry for various bacterial species and cell mass computed from Coulter Counter volume and buoyant density. This agreement validated the standard curve and supported the assumption that cells were aligned in the flow stream. Several subpopulations were resolved in a mixture of three species analyzed according to forward light scatter and DNA-bound DAPI (4′,6-diamidino-2-phenylindole) fluorescence intensity. The total biomass of the mixture was 340 μg/liter. The lowest value for mean dry mass, 0.027 ± 0.008 pg/cell, was for the subpopulation of
C. oligotrophus
containing cells with a single chromosome. Calculations from measurements of dry mass, Coulter Counter volume, and buoyant density revealed that the dry weight of the isolate was 14 to 18% of its wet weight, compared to 30% for
Escherichia coli
. The method is suitable for cells with 0.005 to about 1.2 pg of dry weight at concentrations of as low as 10
3
cells/ml and offers a unique capability for determining biomass distributions in mixed bacterial populations.
Bacterial Stress Responses to 1-Megahertz Pulsed Ultrasound in the Presence of Microbubbles
Authors: Vollmer Amy C. , Kwakye Sylvia , Halpern Matthew , Everbach E. Carr 
Published: December 2019

ABSTRACT

Members of a panel of stress-responsive biosensors have been used to study the effect of megahertz frequency ultrasound on
Escherichia coli
. Insonification causes acoustic cavitation, the collapse of oscillating microbubbles in solution, which can damage bacterial cells. A focused 1-MHz ultrasound transducer, capable of generating a spatial peak pulse average intensity of 500 W/cm
2
, was used to treat liquid bacterial cultures. Stress-responsive promoters fused to
luxCDABE
allowed the continuous measurement of light produced as a result of protein damage, DNA damage, oxidative stress, and membrane perturbation. A promoter responsive to ammonia limitation was not transcriptionally activated under test conditions. In contrast to bacteria in exponentially growing cultures, those in stationary-phase cultures were more resistant to the effects of ultrasound treatment. Quantification of the degree of acoustic cavitation due to symmetric bubble collapse was measured by a 20-MHz passive transducer, the output of which appears to be only partially correlated with cellular damage and survival. The methods and results summarized here provide the basis for further investigation into applications, including the purification of water samples.
PCR-Based Detection of the Causal Agent of Watermark Disease in Willows (
Salix
spp.)
Authors: Hauben L. , Steenackers M. , Swings J. 
Published: December 2019

ABSTRACT

The watermark disease, caused by
Brenneria salicis
(formerly
Erwinia salicis
), is of significant concern wherever tree-forming willows are grown or occur naturally. The movement of infected, asymptomatic cuttings is a major cause of pathogen dispersal. A reliable and sensitive diagnostic procedure is necessary for the safe movement of willow planting material. We derived primers from the nucleotide sequence of the 16S rRNA gene of
B. salicis
for the development of a PCR to detect this pathogen. One set of primers, Es1a-Es4b, directed the amplification of a 553-bp fragment from
B. salicis
genomic DNA as well as
B. salicis
cells. PCR products were not observed when genomic DNA was tested for 27 strains of other, related plant-associated bacteria. Genomic fingerprinting by amplification fragment length polymorphism of
B. salicis
strains, originating from four different countries, and related
Brenneria
,
Pectobacterium
, and
Erwinia
strains revealed a very high similarity among the
B. salicis
genomes, indicating that the spread of the pathogen is mainly due to the transportation of infected cuttings. The PCR had to be preceded by a DNA extraction in order to detect the pathogen in the vascular fluid of willows. The minimum number of cells that could be detected from vascular fluid was 20 CFU/ml. The PCR assays proved to be very sensitive and reliable in detecting
B. salicis
in willow plant material.
Sequence and Secondary Structure of the Mitochondrial Small-Subunit rRNA V4, V6, and V9 Domains Reveal Highly Species-Specific Variations within the Genus
Agrocybe
Authors: Gonzalez Patrice , Labarère Jacques 
Published: December 2019

ABSTRACT

A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus
Agrocybe
by PCR amplification of 42 wild isolates belonging to 10 species,
Agrocybe aegerita
,
Agrocybe dura
,
Agrocybe chaxingu
,
Agrocybe erebia
,
Agrocybe firma
,
Agrocybe praecox
,
Agrocybe paludosa
,
Agrocybe pediades
,
Agrocybe alnetorum
, and
Agrocybe vervacti
. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included
A. aegerita
,
A. chaxingu
, and
A. erebia
; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included
A. pediades
; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included
A. paludosa
,
A. firma
,
A. alnetorum
, and
A. praecox
; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included
A. vervacti
and
A. dura
. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The conservation of the sequences of the V4, V6, and V9 domains of the mitochondrial SSU rRNA within species and the high degree of interspecific variation found in the
Agrocybe
species studied open the way for these sequences to be used as specific molecular markers of the Basidiomycota.
Ratios of Carbon Isotopes in Microbial Lipids as an Indicator of Substrate Usage
Authors: Abraham Wolf-Rainer , Hesse Christian , Pelz Oliver 
Published: December 2019

ABSTRACT

The occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. However, these fatty acids can also be used as indicators of substrate usage. For this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. We grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratios of fatty acids of different lipid fractions. A comparison of the differences of δ
13
C values of palmitic acid (C
16:0
) with the δ
13
C values of the substrates revealed that the isotope ratio is independent of the growth stage and that most microorganisms showed enrichment of C
16:0
with
13
C when growing on glycerol. With the exception of
Burkholderia gladioli
, all microorganism showed depletion of
13
C in C
16:0
while incorporating the carbons of glucose, and most of them were enriched with
13
C from mannose, with the exception of
Pseudomonas fluorescens
and the Zygomycotina. Usually, the glycolipid fractions are depleted in
13
C compared to the phospholipid fractions. The δ
13
C pattern was not uniform within the different fatty acids of a given microbial species. Generally, tetradecanoic acid (C
14:0
) was depleted of
13
C compared to palmitic acid (C
16:0
) while octadecanoic acid (C
18:0
) was enriched. These results are important for the calibration of a new method in which δ
13
C values of fatty acids from the environment delineate the use of bacterial substrates in an ecosystem.
Partial Characterization of theStreptomyces lividans xlnBPromoter and Its Use for Expression of a Thermostable Xylanase fromThermotoga maritima
Authors: Chen Chih-Cheng , Westpheling Janet 
Published: December 2019

ABSTRACTXylanase activity assays were used to screen aStreptomyces coelicolorgenomic library inEscherichia coli, and a xylanase gene that is 99% identical to the xylanase B gene (xlnB) ofS. lividans(GenBank accession no.M64552) was identified. The promoter region of this gene was identified by using a transcriptional fusion between the upstream region of theS. coelicolor xlnBgene and thexylEreporter gene. Transcription from thexlnBpromoter was found to be induced by xylan and repressed by glucose. A single apparent transcription start site was identified by both primer extension analysis and in vitro run off transcription assays. Analysis of deletions of the promoter identified a region required for glucose repression. By using the transcriptional and protein localization signals of theStreptomyces xlnBgene, an in-frame translational fusion between the end of thexlnBsignal sequence and the ATG of theThermotoga maritima xynAgene was constructed. ThexynAgene encodes a thermostable xylanase that has been demonstrated to be useful in the bleaching of Kraft pulp. ThexlnB-xynAgene fusion was expressed inStreptomyces, and the activity of the protein produced was thermostable and was localized to the supernatant fraction of harvested cells.