bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities
Authors: Steven Blaire , Kuske Cheryl R. , Gallegos-Graves La Verne , Reed Sasha C. , Belnap Jayne 
Published: August 2015

ABSTRACT

Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased
Cyanobacteria
abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.
Distribution, Activities, and Interactions of Methanogens and Sulfate-Reducing Prokaryotes in the Florida Everglades
Authors: Bae Hee-Sung , Holmes M. Elizabeth , Chanton Jeffrey P. , Reddy K. Ramesh , Ogram Andrew 
Published: August 2015

ABSTRACT

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (
mcrA
) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO
4
2−
(≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders
Methanomicrobiales
,
Methanosarcinales
,
Methanocellales
,
Methanobacteriales
, and
Methanomassiliicoccales
. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic
Methanomicrobiales
were more numerous than the
Methanosaetaceae
obligatory acetotrophs in SO
4
2−
-rich areas of WCA-2A, while the
Methanosaetaceae
were dominant over the
Methanomicrobiales
in WCA-3A (with relatively low SO
4
2−
concentrations; ≤4 μM). qPCR of
dsrB
sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO
4
2−
(a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [α
app
; defined as (amount of δ
13
CO
2
+ 1,000)/(amount of δ
13
CH
4
+ 1,000)], and higher
Methanosaetaceae
mcrA
transcript levels compared to those for the controls without MoO
4
2−
. These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.
Spatial Patterns of Carbonate Biomineralization in Biofilms
Authors: Li Xiaobao , Chopp David L. , Russin William A. , Brannon Paul T. , Parsek Matthew R. , Packman Aaron I. 
Published: August 2015

ABSTRACT

Microbially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method for
in situ
, real-time imaging of biomineralization in biofilms and use it to show that
Pseudomonas aeruginosa
biofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization produced
in situ
were substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties.
A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria
Authors: Scott Israel M. , Rubinstein Gabe M. , Lipscomb Gina L. , Basen Mirko , Schut Gerrit J. , Rhaesa Amanda M. , Lancaster W. Andrew , Poole Farris L. , Kelly Robert M. , Adams Michael W. W. 
Published: August 2015

ABSTRACT

Caldicellulosiruptor bescii
grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment.
C. bescii
ferments both C
5
and C
6
sugars primarily to hydrogen gas, lactate, acetate, and CO
2
and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the
C. bescii
genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of
C. bescii
has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in
C. bescii
was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon
Pyrococcus furiosus
. Furthermore,
C. bescii
also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in
C. bescii
, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
Identification of the
mcpA
and
mcpM
Genes, Encoding Methyl-Accepting Proteins Involved in Amino Acid and
l
-Malate Chemotaxis, and Involvement of McpM-Mediated Chemotaxis in Plant Infection by Ralstonia pseudosolanacearum (Formerly Ralstonia solanacearum Phylotypes I and III)
Authors: Hida Akiko , Oku Shota , Kawasaki Takeru , Nakashimada Yutaka , Tajima Takahisa , Kato Junichi 
Published: August 2015

ABSTRACT

Sequence analysis has revealed the presence of 22 putative methyl-accepting chemotaxis protein (
mcp
) genes in the
Ralstonia pseudosolanacearum
GMI1000 genome. PCR analysis and DNA sequencing showed that the highly motile
R. pseudosolanacearum
strain Ps29 possesses homologs of all 22
R. pseudosolanacearum
GMI1000
mcp
genes. We constructed a complete collection of single
mcp
gene deletion mutants of
R. pseudosolanacearum
Ps29 by unmarked gene deletion. Screening of the mutant collection revealed that
R. pseudosolanacearum
Ps29 mutants of RSp0507 and RSc0606 homologs were defective in chemotaxis to
l
-malate and amino acids, respectively. RSp0507 and RSc0606 homologs were designated
mcpM
and
mcpA
. While wild-type
R. pseudosolanacearum
strain Ps29 displayed attraction to 16 amino acids, the
mcpA
mutant showed no response to 12 of these amino acids and decreased responses to 4 amino acids. We constructed
mcpA
and
mcpM
deletion mutants of highly virulent
R. pseudosolanacearum
strain MAFF106611 to investigate the contribution of chemotaxis to
l
-malate and amino acids to tomato plant infection. Neither single mutant exhibited altered virulence for tomato plants when tested by root dip inoculation assays. In contrast, the
mcpM
mutant (but not the
mcpA
mutant) was significantly less infectious than the wild type when tested by a sand soak inoculation assay, which requires bacteria to locate and invade host roots from sand. Thus, McpM-mediated chemotaxis, possibly reflecting chemotaxis to
l
-malate, facilitates
R. pseudosolanacearum
motility to tomato roots in sand.
Fluorescence Assay for Evaluating Microbicidal Activity of Hand Antiseptics
Authors: Lopez-Gigosos Rosa M. , Mariscal Alberto , Mariscal-Lopez Eloisa , Gutierrez-Bedmar Mario , Fernandez Joaquin 
Published: August 2015

ABSTRACT

We developed a fluorescent β-
d
-glucuronidase activity (BGA)-based assay for detecting and quantifying
Escherichia coli
in samples to assess the biocide efficacy of hand antiseptics. The fluorescence level is proportional to the number of viable
E. coli
organisms present. We compared our assay results to those of the
E. coli
plate count method specified by the European standard for testing hygienic hand rub disinfectant products (EN1500). The plate count method requires excessive handling and materials and is not valid if the number of organisms per plate is too low or high for counting in many of the samples. We optimized the fluorescent assay based on the cleavage of 4-methylumbelliferyl-β-
d
-glucuronide by adding 4-nitrophenyl-β-
d
-glucuronide, a nonfluorogenic BGA substrate, to induce glucuronidase activity and reduce assay time. Furthermore, our method can be automated and eliminates the need for multiple dilutions. Fluorescence was temporally monitored, and the time required to reach a specific value of fluorescence was correlated with the initial number of viable
E. coli
organisms on the samples. There was a positive correlation (
P
< 0.05) with a high correlation coefficient (
R
2
= 0.82) between the
E. coli
counts by plate count and fluorescence methods. Reported effects in fluorescent BGA were compared to the EN1500 plate count method with five hand disinfectants. We found our method more advantageous, because it was as sensitive as the EN1500 method, requires less time to complete, and is less expensive and less laborious than conventional plating techniques.
The Gastrointestinal Tract as a Potential Infection Reservoir of Digital Dermatitis-Associated Treponemes in Beef Cattle and Sheep
Authors: Sullivan L. E. , Carter S. D. , Duncan J. S. , Grove-White D. H. , Angell J. W. , Evans N. J. 
Published: August 2015

ABSTRACT

Digital dermatitis (DD) is an important cause of lameness in dairy cattle worldwide. It has now been reported in beef cattle and also sheep (contagious ovine digital dermatitis [CODD]). Three
Treponema
phylogroups are consistently isolated from lesions,
Treponema medium-
like,
Treponema phagedenis
-like, and
Treponema pedis
. The gastrointestinal (GI) tract and feces are suggested sites of treponemal infection in dairy cattle; however, isolation of DD-associated treponemes from these areas has previously failed. This study surveyed gingival tissues, rectal tissues, and feces of beef cattle and sheep for the molecular presence (PCR) and isolation of the three cultivable DD-treponeme phylogroups. Of the sheep gingival (
n
= 40) and rectal (
n
= 40) tissues, 1/40 gingival tissues was positive for DD-associated treponemes (
T. pedis
), as were 3/40 rectal tissues (one containing
T. medium-
like and two containing
T. pedis
). No DD-associated treponeme DNA was amplified from beef cattle rectal tissues (
n
= 40); however, 4/40 beef gingival tissues were positive for DD-associated treponemes (all containing
T. phagedenis
-like). A
T. phagedenis
-like DD-associated treponeme was isolated from the rectal tissue of a CODD symptomatic sheep. Beef cattle (
n
= 41) and sheep (
n
= 79) feces failed to amplify DD-associated
Treponema
DNA. Twenty-two treponemes were isolated from sheep feces; however, upon phylogenetic analysis, these clustered with the considered nonpathogenic treponemes. This study detected DD-associated treponemes in the GI tract tissues of sheep and beef cattle and successfully isolated a DD-associated treponeme from ruminant rectal tissue. This gives evidence that the GI tract is an important infection reservoir of DD-associated treponemes in multiple DD-infected species.
Hypothetical Protein Avin_16040 as the S-Layer Protein of Azotobacter vinelandii and Its Involvement in Plant Root Surface Attachment
Authors: Liew Pauline Woan Ying , Jong Bor Chyan , Najimudin Nazalan 
Published: August 2015

ABSTRACT

A proteomic analysis of a soil-dwelling, plant growth-promoting
Azotobacter vinelandii
strain showed the presence of a protein encoded by the hypothetical
Avin_16040
gene when the bacterial cells were attached to the
Oryza sativa
root surface. An
Avin_16040
deletion mutant demonstrated reduced cellular adherence to the root surface, surface hydrophobicity, and biofilm formation compared to those of the wild type. By atomic force microscopy (AFM) analysis of the cell surface topography, the deletion mutant displayed a cell surface architectural pattern that was different from that of the wild type.
Escherichia coli
transformed with the wild-type
Avin_16040
gene displayed on its cell surface organized motifs which looked like the S-layer monomers of
A. vinelandii
. The recombinant
E. coli
also demonstrated enhanced adhesion to the root surface.
pH Tolerance in Freshwater Bacterioplankton: Trait Variation of the Community as Measured by Leucine Incorporation
Authors: Bååth Erland , Kritzberg Emma 
Published: August 2015

ABSTRACT

pH is an important factor determining bacterial community composition in soil and water. We have directly determined the community tolerance (trait variation) to pH in communities from 22 lakes and streams ranging in pH from 4 to 9 using a growth-based method not relying on distinguishing between individual populations. The pH in the water samples was altered to up to 16 pH values, covering
in situ
pH ± 2.5 U, and the tolerance was assessed by measuring bacterial growth (Leu incorporation) instantaneously after pH adjustment. The resulting unimodal response curves, reflecting community tolerance to pH, were well modeled with a double logistic equation (mean
R
2
= 0.97). The optimal pH for growth (pH
opt
) among the bacterial communities was closely correlated with
in situ
pH, with a slope (0.89 ± 0.099) close to unity. The pH interval, in which growth was ≥90% of that at pH
opt
, was 1.1 to 3 pH units wide (mean 2.0 pH units). Tolerance response curves of communities originating from circum-neutral pH were symmetrical, whereas in high-pH (8.9) and especially in low-pH (<5.5) waters, asymmetric tolerance curves were found. In low-pH waters, decreasing pH was more detrimental for bacterial growth than increasing pH, with a tendency for the opposite for high-pH waters. A pH tolerance index, using the ratio of growth at only two pH values (pH 4 and 8), was closely related to pH
opt
(
R
2
= 0.83), allowing for easy determination of pH tolerance during rapid changes in pH.
Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen
Authors: Kittelmann Sandra , Kirk Michelle R. , Jonker Arjan , McCulloch Alan , Janssen Peter H. 
Published: August 2015

ABSTRACT

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (
R
= 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (
R
= 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.
Anaerobic Growth of Corynebacterium glutamicum via Mixed-Acid Fermentation
Authors: Michel Andrea , Koch-Koerfges Abigail , Krumbach Karin , Brocker Melanie , Bott Michael 
Published: August 2015

ABSTRACT

Corynebacterium glutamicum
, a model organism in microbial biotechnology, is known to metabolize glucose under oxygen-deprived conditions to
l
-lactate, succinate, and acetate without significant growth. This property is exploited for efficient production of lactate and succinate. Our detailed analysis revealed that marginal growth takes place under anaerobic conditions with glucose, fructose, sucrose, or ribose as a carbon and energy source but not with gluconate, pyruvate, lactate, propionate, or acetate. Supplementation of glucose minimal medium with tryptone strongly enhanced growth up to a final optical density at 600 nm (OD
600
) of 12, whereas tryptone alone did not allow growth. Amino acids with a high ATP demand for biosynthesis and amino acids of the glutamate family were particularly important for growth stimulation, indicating ATP limitation and a restricted carbon flux into the oxidative tricarboxylic acid cycle toward 2-oxoglutarate. Anaerobic cultivation in a bioreactor with constant nitrogen flushing disclosed that CO
2
is required to achieve maximal growth and that the pH tolerance is reduced compared to that under aerobic conditions, reflecting a decreased capability for pH homeostasis. Continued growth under anaerobic conditions indicated the absence of an oxygen-requiring reaction that is essential for biomass formation. The results provide an improved understanding of the physiology of
C. glutamicum
under anaerobic conditions.
Differences in Host Innate Responses among Coccidioides Isolates in a Murine Model of Pulmonary Coccidioidomycosis
Authors: Lewis Eric R. G. , David Victoria R. , Doyle Adina L. , Rajabi Khadijeh , Kiefer Jeffrey A. , Pirrotte Patrick , Barker Bridget M. 
Published: August 2015

ABSTRACTCoccidioides immitisandCoccidioides posadasiiare soil-dwelling fungi and the causative agents of coccidioidomycosis, a mycosis endemic to certain semiarid regions in the Americas. The most common route of infection is by inhalation of airborneCoccidioidesarthroconidia. Once a susceptible host inhales the conidia, a transition to mature endosporulated spherules can occur within the first 5 days of infection. For this study, we examined the host response in a murine model of coccidioidomycosis during a time period of infection that has not been well characterized. We collected lung tissue and bronchoalveolar lavage fluid (BALF) from BALB/c mice that were infected with aC. immitispure strain, aC. immitishybrid strain, or aC. posadasiistrain as well as uninfected mice. We compared the host responses to theCoccidioidesstrains used in this study by assessing the level of transcription of selected cytokine genes in lung tissues and characterized host and fungal proteins present in BALF. Host response varied depending on theCoccidioidesstrain that was used and did not appear to be overly robust. This study provides a foundation to begin to dissect the host immune response early in infection, to detect abundantCoccidioidesproteins, and to develop diagnostics that target these early time points of infection.
Steroid-sensitive nephrotic syndrome: an evidence-based update of immunosuppressive treatment in children
Authors: Larkins Nicholas , Kim Siah , Craig Jonathan , Hodson Elisabeth 
Published: August 2015

Nephrotic syndrome is one of the most common paediatric glomerular diseases, with an incidence of around two per 100 000 children per year. Corticosteroids are the mainstay of treatment, with 85%–90% of children going into remission with an 8-week course of treatment. Unfortunately, nephrotic syndrome follows a relapsing and remitting course in the majority, with 90% relapsing at least once. About half will progress to frequently relapsing nephrotic syndrome (FRNS) or steroid-dependent nephrotic syndrome (SDNS). Different initial steroid regimens have been evaluated since the first trials in Europe and America in the 1960s. Most trials have been designed to evaluate the optimal duration of the initial therapy, rather than different cumulative doses of corticosteroid, or the management of relapses. Until recently, these data suggested that an initial treatment duration of up to 6 months reduced the number of children developing a relapse, without evidence of increased steroid toxicity. Recently, three large, well-designed randomised control trials were published, which demonstrated no significant reduction in risk of relapse or of developing FRNS by extended treatment compared with 2 or 3 months. While there are few trial data to guide the treatment of individual relapses in steroid-sensitive nephrotic syndrome (SSNS), there is some evidence that a short course of corticosteroid therapy during upper respiratory tract infection may prevent relapse. In patients with FRNS or SDNS who continue to relapse despite low-dose alternate-day steroids a number of non-corticosteroid, steroid-sparing immunosuppressive agents (cyclophosphamide, ciclosporin, tacrolimus, mycophenolate mofetil, levamisole, rituximab) have been shown to reduce the risk of relapse and of FRNS. However, there are limited head-to-head data to inform which agent should be preferred. In this article, we review recent data from randomised trials to update paediatricians on the current evidence supporting interventions in SSNS.