bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen, Carbon, and Sulfur Metabolism in Natural
Thioploca
Samples
Authors: Otte Sandra , Kuenen J. Gijs , Nielsen Lars P. , Paerl Hans W. , Zopfi Jakob , Schulz Heide N. , Teske Andreas , Strotmann Bettina , Gallardo Victor A. , Jørgensen Bo B. 
Published: December 2019

ABSTRACT

Filamentous sulfur bacteria of the genus
Thioploca
occur as dense mats on the continental shelf off the coast of Chile and Peru. Since little is known about their nitrogen, sulfur, and carbon metabolism, this study was undertaken to investigate their (eco)physiology.
Thioploca
is able to store internally high concentrations of sulfur globules and nitrate. It has been previously hypothesized that these large vacuolated bacteria can oxidize sulfide by reducing their internally stored nitrate. We examined this nitrate reduction by incubation experiments of washed
Thioploca
sheaths with trichomes in combination with
15
N compounds and mass spectrometry and found that these
Thioploca
samples produce ammonium at a rate of 1 nmol min
−1
mg of protein
−1
. Controls showed no significant activity. Sulfate was shown to be the end product of sulfide oxidation and was observed at a rate of 2 to 3 nmol min
−1
mg of protein
−1
. The ammonium and sulfate production rates were not influenced by the addition of sulfide, suggesting that sulfide is first oxidized to elemental sulfur, and in a second independent step elemental sulfur is oxidized to sulfate. The average sulfide oxidation rate measured was 5 nmol min
−1
mg of protein
−1
and could be increased to 10.7 nmol min
−1
mg of protein
−1
after the trichomes were starved for 45 h. Incorporation of
14
CO
2
was at a rate of 0.4 to 0.8 nmol min
−1
mg of protein
−1
, which is half the rate calculated from sulfide oxidation. [2-
14
C]acetate incorporation was 0.4 nmol min
−1
mg of protein
−1
, which is equal to the CO
2
fixation rate, and no
14
CO
2
production was detected. These results suggest that
Thioploca
species are facultative chemolithoautotrophs capable of mixotrophic growth. Microautoradiography confirmed that
Thioploca
cells assimilated the majority of the radiocarbon from [2-
14
C]acetate, with only a minor contribution by epibiontic bacteria present in the samples.
Development of Bacterial Contamination during Production of Yeast Extracts
Authors: Barrette Julie , Champagne Claude P. , Goulet Jacques 
Published: December 2019

ABSTRACTBaker’s yeast suspensions having bacterial populations of 106and 108CFU/ml were subjected to autolysis processes designed to obtain yeast extracts (YE). The bacterial contaminants added to the yeast cell suspensions were produced with spent broths obtained from a commercial yeast production plant and contained 59% cocci (Leuconostoc,Aerococcus,Lactococcus) as well as 41% bacilli (Bacillus). Autolyses were conducted at four different pH levels (4.0, 5.5, 7.0, and 8.5) and with two autolysis-promoting agents (ethyl acetate and chitosan). Processing parameters were more important than the initial bacterial population in the development of contaminating bacteria during manufacture of YE. Drops in the viable bacterial population after a 24-h autolysis were observed when pH was adjusted to 4.0 or when ethyl acetate was added. A significant interaction was found between the effects of pH and autolysis promoters on the bacterial population in YE, indicating that the activity of ethyl acetate, as opposed to that of chitosan, was not influenced by pH.
Low-Molecular-Weight Sulfonates, a Major Substrate for Sulfate Reducers in Marine Microbial Mats
Authors: Visscher Pieter T. , Gritzer Rachel F. , Leadbetter Edward R. 
Published: December 2019

ABSTRACTSeveral low-molecular-weight sulfonates were added to microbial mat slurries to investigate their effects on sulfate reduction. Instantaneous production of sulfide occurred after taurine and cysteate were added to all of the microbial mats tested. The rates of production in the presence of taurine and cysteate were 35 and 24 μM HS−h−1in a stromatolite mat, 38 and 36 μM HS−h−1in a salt pond mat, and 27 and 18 μM HS−h−1in a salt marsh mat, respectively. The traditionally used substrates lactate and acetate stimulated the rate of sulfide production 3 to 10 times more than taurine and cysteate stimulated the rate of sulfide production in all mats, but when ethanol, glycolate, and glutamate were added to stromatolite mat slurries, the resulting increases were similar to the increases observed with taurine and cysteate. Isethionate, sulfosuccinate, and sulfobenzoate were tested only with the stromatolite mat slurry, and these compounds had much smaller effects on sulfide production. Addition of molybdate resulted in a greater inhibitory effect on acetate and lactate utilization than on sulfonate use, suggesting that different metabolic pathways were involved. In all of the mats tested taurine and cysteate were present in the pore water at nanomolar to micromolar concentrations. An enrichment culture from the stromatolite mat was obtained on cysteate in a medium lacking sulfate and incubated anaerobically. The rate of cysteate consumption by this enrichment culture was 1.6 pmol cell−1h−1. Compared to the results of slurry studies, this rate suggests that organisms with properties similar to the properties of this enrichment culture are a major constituent of the sulfidogenic population. In addition, taurine was consumed at some of highest dilutions obtained from most-probable-number enrichment cultures obtained from stromatolite samples. Based on our comparison of the sulfide production rates found in various mats, low-molecular-weight sulfonates are important sources of C and S in these ecosystems.
Nanomolar Levels of Dimethylsulfoniopropionate, Dimethylsulfonioacetate, and Glycine Betaine Are Sufficient To Confer Osmoprotection to
Escherichia coli
Authors: Cosquer Anne , Pichereau Vianney , Pocard Jean-Alain , Minet Jacques , Cormier Michel , Bernard Théophile 
Published: December 2019

ABSTRACT

We combined the use of low inoculation titers (300 ± 100 CFU/ml) and enumeration of culturable cells to measure the osmoprotective potentialities of dimethylsulfoniopropionate (DMSP), dimethylsulfonioacetate (DMSA), and glycine betaine (GB) for salt-stressed cultures of
Escherichia coli
. Dilute bacterial cultures were grown with osmoprotectant concentrations that encompassed the nanomolar levels of GB and DMSP found in nature and the millimolar levels of osmoprotectants used in standard laboratory osmoprotection bioassays. Nanomolar concentrations of DMSA, DMSP, and GB were sufficient to enhance the salinity tolerance of
E. coli
cells expressing only the ProU high-affinity general osmoporter. In contrast, nanomolar levels of osmoprotectants were ineffective with a mutant strain (GM50) that expressed only the low-affinity ProP osmoporter. Transport studies showed that DMSA and DMSP, like GB, were taken up via both ProU and ProP. Moreover, ProU displayed higher affinities for the three osmoprotectants than ProP displayed, and ProP, like ProU, displayed much higher affinities for GB and DMSA than for DMSP. Interestingly, ProP did not operate at substrate concentrations of 200 nM or less, whereas ProU operated at concentrations ranging from 1 nM to millimolar levels. Consequently,
proU
+
strains of
E. coli
, but not the
proP
+
strain GM50, could also scavenge nanomolar levels of GB, DMSA, and DMSP from oligotrophic seawater. The physiological and ecological implications of these observations are discussed.
Kinetics, Stereospecificity, and Expression of the Malolactic Enzyme
Authors: Arthurs Ceri E. , Lloyd David 
Published: December 2019

ABSTRACT

Mass spectrometric measurement of carbon dioxide production was used to study malolactic fermentation (MLF) in
Lactobacillus collinoides
isolated from cider. The kinetics and stereospecificity of the malolactic enzyme (MLE) were studied, and the stoichiometry of the reaction sequence was investigated. The optimum pH for activity of the MLE was 4.9. MLF was more rapid (in both intact cells and cell extracts) when
l
-malic acid was used than when
d
-malic acid or the racemic mixture was added. The enzyme was found to be constitutively present in
L. collinoides
. Addition of
l
-malic acid (37 mM) to the growth medium resulted in increased MLE activity; addition of the
d
isomer alone or the racemic mixture resulted in lower activities. Addition of the main sugars in apple juice (fructose, sucrose, and glucose) to the growth medium in the presence of malic acid repressed production of MLE to similar extents in all three cases; in the absence of malic acid, instead of inhibiting MLF, addition of sugars to the growth medium somewhat increased the residual MLE activity.
Isolation, Characterization, and Avenacin Sensitivity of a Diverse Collection of Cereal-Root-Colonizing Fungi
Authors: Carter Jon P. , Spink John , Cannon Paul F. , Daniels Michael J. , Osbourn Anne E. 
Published: December 2019

ABSTRACT
A total of 161 fungal isolates were obtained from the surface-sterilized roots of field-grown oat and wheat plants in order to investigate the nature of the root-colonizing fungi supported by these two cereals. Fungi were initially grouped according to their colony morphologies and then were further characterized by ribosomal DNA sequence analysis. The collection contained a wide range of ascomycetes and also some basidiomycete fungi. The fungi were subsequently assessed for their abilities to tolerate and degrade the antifungal oat root saponin, avenacin A-1. Nearly all the fungi obtained from oat roots were avenacin A-1 resistant, while both avenacin-sensitive and avenacin-resistant fungi were isolated from the roots of the non-saponin-producing cereal, wheat. The majority of the avenacin-resistant fungi were able to degrade avenacin A-1. These experiments suggest that avenacin A-1 is likely to influence the development of fungal communities within (and possibly also around) oat roots.
Optical Characteristics of the Phototroph
Thiocapsa roseopersicina
and Implications for Real-Time Monitoring of the Bacteriochlorophyll Concentration
Authors: Gitelson A. , Stark R. , Dor I. , Michelson O. , Yacobi Y. Z. 
Published: December 2019

ABSTRACT

Optical characteristics of a
Thiocapsa roseopersicina
culture and environmental samples containing
T. roseopersicina
were investigated in the spectral range of 400 to 1,100 nm (absorption coefficient, diffuse attenuation coefficient, and reflectance). Specific absorption coefficients of
T. roseopersicina
at wavelengths of 480, 520, 550, 580, 805, 860, and 880 nm were determined. It is suggested that the optical properties of
T. roseopersicina
in the near-infrared range of 800 to 930 nm, confirmed in this study, may be used for development of remote sensing techniques for real-time monitoring of
T. roseopersicina
and other bacteriochlorophyll
a
-containing microbes.
Use of Antibiotic Resistance Analysis To Identify Nonpoint Sources of Fecal Pollution
Authors: Wiggins B. A. , Andrews R. W. , Conway R. A. , Corr C. L. , Dobratz E. J. , Dougherty D. P. , Eppard J. R. , Knupp S. R. , Limjoco M. C. , Mettenburg J. M. , Rinehardt J. M. , Sonsino J. , Torrijos R. L. , Zimmerman M. E. 
Published: December 2019

ABSTRACT
A study was conducted to determine the reliability and repeatability of antibiotic resistance analysis as a method of identifying the sources of fecal pollution in surface water and groundwater. Four large sets of isolates of fecal streptococci (from 2,635 to 5,990 isolates per set) were obtained from 236 samples of human sewage and septage, cattle and poultry feces, and pristine waters. The patterns of resistance of the isolates to each of four concentrations of up to nine antibiotics were analyzed by discriminant analysis. When isolates were classified individually, the average rate of correct classification (ARCC) into four possible types (human, cattle, poultry, and wild) ranged from 64 to 78%. When the resistance patterns of all isolates from each sample were averaged and the resulting sample-level resistance patterns were classified, the ARCCs were much higher (96 to 100%). These data confirm that there are measurable and consistent differences in the antibiotic resistance patterns of fecal streptococci isolated from various sources of fecal pollution and that antibiotic resistance analysis can be used to classify and identify these sources.
Chloramphenicol Inhibition of Denitrifying Enzyme Activity in Two Agricultural Soils
Authors: Murray Robert E. , Knowles Roger 
Published: December 2019

ABSTRACT

Chloramphenicol, at concentrations greater than 0.1 g/liter (0.3 mM), inhibited the denitrifying enzyme activity (DEA) of slurries of humisol and sandy loam soils by disrupting the activity of existing nitrate reductase enzymes. When the concentration of chloramphenicol was increased from 0.1 to 2.0 g/liter (6.0 mM), the rate of nitrite production from nitrate decreased by 25 to 46%. The rate of NO production from nitrate decreased by 20 to 39%, and the rate of N
2
O production from nitrate, in the presence of acetylene (DEA), decreased by 21 to 61%. The predicted values of DEA at 0 g of chloramphenicol/liter computed from linear regressions of DEA versus chloramphenicol concentration were 18 to 43% lower than DEA measurements made in the absence of chloramphenicol and within a few per cent of DEA rates measured in the presence of 0.1 g of chloramphenicol/liter. We conclude that DEA assays should be carried out with a single (0.1-g/liter) chloramphenicol concentration. Chloramphenicol at concentrations greater than 0.1 g/liter inhibits the activity of existing denitrifying enzymes and should not be used in DEA assays.
Depth Penetration and Detection of pH Gradients in Biofilms by Two-Photon Excitation Microscopy
Authors: Vroom Jurrien M. , De Grauw Kees J. , Gerritsen Hans C. , Bradshaw David J. , Marsh Philip D. , Watson G. Keith , Birmingham John J. , Allison Clive 
Published: December 2019

ABSTRACT

Deep microbial biofilms are a major problem in many industrial, environmental, and medical settings. Novel approaches are needed to understand the structure and metabolism of these biofilms. Two-photon excitation microscopy (TPE) and conventional confocal laser scanning microscopy (CLSM) were compared quantitatively for the ability to visualize bacteria within deep in vitro biofilms. pH gradients within these biofilms were determined by fluorescence lifetime imaging, together with TPE. A constant-depth film fermentor (CDFF) was inoculated for 8 h at 50 ml · h
−1
with a defined mixed culture of 10 species of bacteria grown in continuous culture. Biofilms of fixed depths were developed in the CDFF for 10 or 11 days. The microbial compositions of the biofilms were determined by using viable counts on selective and nonselective agar media; diverse mixed-culture biofilms developed, including aerobic, facultative, and anaerobic species. TPE was able to record images four times deeper than CLSM. Importantly, in contrast to CLSM images, TPE images recorded deep within the biofilm showed no loss of contrast. The pH within the biofilms was measured directly by means of fluorescence lifetime imaging; the fluorescence decay of carboxyfluorescein was correlated with biofilm pH and was used to construct a calibration curve. pH gradients were detectable, in both the lateral and axial directions, in steady-state biofilms. When biofilms were overlaid with 14 mM sucrose for 1 h, distinct pH gradients developed. Microcolonies with pH values of below pH 3.0 were visible, in some cases adjacent to areas with a much higher pH (>5.0). TPE allowed resolution of images at significantly greater depths (as deep as 140 μm) than were possible with CLSM. Fluorescence lifetime imaging allowed the in situ, real-time imaging of pH and the detection of sharp gradients of pH within microbial biofilms.
Use of Single-Strand Conformation Polymorphism Analysis To Examine the Variability of the
rpoS
Sequence in Environmental Isolates of Salmonellae
Authors: Jordan Suzanne J. , Dodd Christine E. R. , Stewart Gordon S. A. B. 
Published: December 2019

ABSTRACT

The natural environment places its resident microflora under stress, which may often result in adaptation by the microflora in order to increase the probability of survival. One such mechanism that has been postulated involves
rpoS
, which encodes a sigma factor that is known to enhance survival upon exposure to stress. The present work aimed to examine the genetic variability of
rpoS
in a selection of
Salmonella enterica
subspecies environmental isolates with an automated single-strand conformation polymorphism analysis technique. The results indicated that sequence variation does occur and that these changes are mainly located in two areas: at the center and near the end of the coding region. The variability was generally at the single-base level, although one strain (
S. arizonae
) did demonstrate significant differences in nucleotide sequence.
Distribution and Evolution of the Xylanase Genes
xynA
and
xynB
and Their Homologues in Strains of
Butyrivibrio fibrisolvens
Authors: Dalrymple Brian P. , Swadling Yolande , Layton Ingrid , Gobius Kari S. , Xue Gang-Ping 
Published: December 2019

ABSTRACT

The ruminal bacterium
Butyrivibrio fibrisolvens
is being engineered by the introduction of heterologous xylanase genes in an attempt to improve the utilization of plant material in ruminants. However, relatively little is known about the diversity and distribution of the native xylanase genes in strains of
B. fibrisolvens
. In order to identify the most appropriate hosts for such modifications, the xylanase genotypes of 28 strains from the three 16S ribosomal DNA (rDNA) subgroups of
Butyrivibrio fibrisolvens
have been investigated. Only 4 of the 20 strains from 16S rDNA group 2 contained homologues of the strain Bu49
xynA
gene. However, these four
xynA
-containing strains, and two other group 2 strains, contained members of a second xylanase gene family clearly related to
xynA
(subfamily I). Homologues of
xynB
, a second previously described xylanase gene from
B. fibrisolvens
, were identified only in three of the seven group 1 strains and not in the group 2 and 3 strains. However, six of the group 1 strains contained one or more members of the two subfamilies of homologues of
xynA
. The distribution of genes and the nucleotide sequence relationships between the members of the two
xynA
subfamilies are consistent with the progenitor of all strains of
B. fibrisolvens
having contained a
xynA
subfamily I gene. Since many xylanolytic strains of
B. fibrisolvens
did not contain members of either of the
xynA
subfamilies or of the
xynB
family, at least one additional xylanase gene family remains to be identified in
B. fibrisolvens
.
How Stable Is Stable? Function versus Community Composition
Authors: Fernández Ana , Huang Suiying , Seston Sherry , Xing Jian , Hickey Robert , Criddle Craig , Tiedje James 
Published: December 2019

ABSTRACT

The microbial community dynamics of a functionally stable, well-mixed, methanogenic reactor fed with glucose were analyzed over a 605-day period. The reactor maintained constant pH and chemical oxygen demand removal during this period. Thirty-six
rrn
clones from each of seven sampling events were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) for the
Bacteria
and
Archaea
domains and by sequence analysis of dominant members of the community. Operational taxonomic units (OTUs), distinguished as unique ARDRA patterns, showed reproducible distribution for three sample replicates. The highest diversity was observed in the
Bacteria
domain. The 16S ribosomal DNA
Bacteria
clone library contained 75 OTUs, with the dominant OTU accounting for 13% of the total clones, but just 21
Archaea
OTUs were found, and the most prominent OTU represented 50% of the clones from the respective library. Succession in methanogenic populations was observed, and two periods were distinguished: in the first,
Methanobacterium formicicum
was dominant, and in the second,
Methanosarcina mazei
and a
Methanobacterium bryantii
-related organism were dominant. Higher variability in
Bacteria
populations was detected, and the temporal OTU distribution suggested a chaotic pattern. Although dominant OTUs were constantly replaced from one sampling point to the next, phylogenetic analysis indicated that inferred physiologic changes in the community were not as dramatic as were genetic changes. Seven of eight dominant OTUs during the first period clustered with the spirochete group, although a cyclic pattern of substitution occurred among members within this order. A more flexible community structure characterized the second period, since a sequential replacement of a
Eubacterium
-related organism by an unrelated deep-branched organism and finally by a
Propionibacterium
-like species was observed. Metabolic differences among the dominant fermenters detected suggest that changes in carbon and electron flow occurred during the stable performance and indicate that an extremely dynamic community can maintain a stable ecosystem function.
Inactivation ofMXR1Abolishes Formation of Dimethyl Sulfide from Dimethyl Sulfoxide inSaccharomyces cerevisiae
Authors: Hansen Jørgen 
Published: December 2019

ABSTRACTDimethyl sulfide (DMS) is a sulfur compound of importance for the organoleptic properties of beer, especially some lager beers. Synthesis of DMS during beer production occurs partly during wort production and partly during fermentation. Methionine sulfoxide reductases are the enzymes responsible for reduction of oxidized cellular methionines. These enzymes have been suggested to be able to reduce dimethyl sulfoxide (DMSO) as well, with DMS as the product. A gene for an enzymatic activity leading to methionine sulfoxide reduction inSaccharomycesyeast was recently identified. We confirmed that theSaccharomyces cerevisiaeopen reading frame YER042w appears to encode a methionine sulfoxide reductase, and propose the nameMXR1for the gene. We found that Mxr1p catalyzes reduction of DMSO to DMS and that anmxr1disruption mutant cannot reduce DMSO to DMS. Mutant strains appear to have unchanged fitness under several laboratory conditions, and in this paper I hypothesize that disruption ofMXR1in brewing yeasts would neutralize the contribution of the yeast to the DMS content in beer.
High Bacterial Diversity in Permanently Cold Marine Sediments
Authors: Ravenschlag Katrin , Sahm Kerstin , Pernthaler Jakob , Amann Rudolf 
Published: December 2019

ABSTRACT

A 16S ribosomal DNA (rDNA) clone library from permanently cold marine sediments was established. Screening 353 clones by dot blot hybridization with group-specific oligonucleotide probes suggested a predominance of sequences related to bacteria of the sulfur cycle (43.4% potential sulfate reducers). Within this fraction, the major cluster (19.0%) was affiliated with
Desulfotalea
sp. and other closely related psychrophilic sulfate reducers isolated from the same habitat. The cloned sequences showed between 93 and 100% similarity to these bacteria. Two additional groups were frequently encountered: 13% of the clones were related to
Desulfuromonas palmitatis
, and a second group was affiliated with
Myxobacteria
spp. and
Bdellovibrio
spp. Many clones (18.1%) belonged to the γ subclass of the class
Proteobacteria
and were closest to symbiotic or free-living sulfur oxidizers. Probe target groups were further characterized by amplified rDNA restriction analysis to determine diversity within the groups and within the clone library. Rarefaction analysis suggested that the total diversity assessed by 16S rDNA analysis was very high in these permanently cold sediments and was only partially revealed by screening of 353 clones.