sp. nov., a novel species of the family isolated from chicken faeces.

A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04, was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus and was most closely related to CCUG 53761A (97.

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.

Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly.

TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.

Dysbiosis of the gut microbiome via antibiotics, changes in diet and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period.

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness.

Unlabelled: We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases.

Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge.

Although the antimicrobial capabilities of silver nanoparticles (AgNPs) are widely reported, their impacts on ecologically important microbial communities are not well understood. AgNPs released from consumer products will likely enter sewer systems and wastewater treatment plants, where they would encounter (and potentially upset) activated sludge (AS), a complex ecosystem containing a variety of bacteria. Herein we address the effects of AgNPs and Ag(+) ions on the microbial community structure of AS, using pyrosequencing technology.

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.

Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes.

Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.

Unlabelled: Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (nifH). We obtained 1.

Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate.

To minimize the change of lignocellulosic hydrolysate composition during storage, the effects of storage conditions (temperature, pH and time) on the composition and fermentability of hydrolysate prepared from AFEX™ (Ammonia Fiber Expansion - a trademark of MBI, Lansing, MI) pretreated corn stover were investigated. Precipitates formed during hydrolysate storage increased with increasing storage pH and time. The precipitate amount was the least when hydrolysate was stored at 4 °C and pH 4.

Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments.

Methane (CH(4)) emitted from high-latitude lakes accounts for 2-6% of the global atmospheric CH(4) budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH(4) that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sediments (0-25 cm) from an arctic tundra lake (Lake Qalluuraq) on the north slope of Alaska and a subarctic taiga lake (Lake Killarney) in Alaska's interior.

Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses.

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression.

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes.

Methane (CH(4)) flux to the atmosphere is mitigated via microbial CH(4) oxidation in sediments and water. As arctic temperatures increase, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is important to predicting future CH(4) emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), and pyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska.

Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing.

Arctic lakes are a significant source of the greenhouse gas methane (CH(4) ), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH(4) flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0-1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH(4) oxidation potential was observed in the upper sediment (0-1 cm depth) with 1.

DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment.

Stable isotope probing with [(13)C]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [(13)C]DNA after a 14-day incubation with [(13)C]biphenyl revealed the dominant organisms to be members of the genera Achromobacter and Pseudomonas. A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [(13)C]DNA fraction revealed two sequence groups similar to bphA (encoding biphenyl dioxygenase) of Comamonas testosteroni strain B-356 and of Rhodococcus sp.

Stimulatory effects of a microbially dechlorinated polychlorinated biphenyl (PCB) mixture on rat uterine contraction in vitro.

Microbially mediated reductive dechlorination has been advocated as the first part of a two-stage (anaerobic/aerobic) biotreatment process for polychlorinated biphenyls (PCBs) in sediments, and is generally viewed as a detoxication process. However, previous studies suggest that microbial dechlorination increases the ability to stimulate uterine contractions compared with the original PCB mixtures. Here, we investigate the composition and uterotonic activity of the commercial PCB mixture Aroclor 1260 before and after incubation with microorganisms eluted from PCB-contaminated sediment of the Hudson River.

Intestinal protozoa are hypothesized to stimulate immunosurveillance against colon cancer.

Colon cancer in humans results in considerable morbidity and mortality throughout most of the world. During the twentieth century, there was a rapid rise in colon cancer within modernizing countries that has not been adequately explained, although the role of diet has been widely explored. Previously, we showed that the presence of the endemic Eimeria spp.

Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.

The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl.

Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb).

Burkholderia xenovorans strain LB400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic ortho dehalogenation (ohb) operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. A two-stage anaerobic/aerobic biotreatment process for Aroclor 1242-contaminated sediment was simulated, and the degradation activities and genetic stabilities of LB400(ohb) and the previously constructed strain RHA1(fcb), capable of growth on 4-chlorobenzoate, were monitored during the aerobic phase. The population dynamics of both strains were also followed by selective plating and real-time PCR, with comparable results; populations of both recombinants increased in the contaminated sediment.

Long-term recovery of PCB-contaminated sediments at the Lake Hartwell superfund site: PCB dechlorination. 2. Rates and extent.

This paper reports on extensive polychlorinated biphenyl (PCB) dechlorination measured in Lake Hartwell (Pickens County, SC) sediments. Vertical sediment cores were collected from 18 locations in Lake Hartwell (Pickens County, SC) and analyzed in 5-cm increments for PCB congeners. The preferential loss of meta and para chlorines with sediment depth demonstrated that PCBs in the sediments underwent reductive dechlorination after burial.

Long-term recovery of PCB-contaminated sediments at the Lake Hartwell superfund site: PCB dechlorination. 1. End-member characterization.

Under anaerobic conditions, such as those typically found in buried sediments, the primary metabolic pathway for polychlorinated biphenyls (PCBs) is reductive dechlorination in which chlorine removal and substitution with hydrogen by bacteria result in a reduced organic compound with fewer chlorines. Vertical sediment cores were collected from Lake Hartwell (Pickens County, SC) and analyzed in 5-cm intervals for 107 PCB congeners in a total of more than 280 samples from 18 sediment cores and surface samples. This paper reports on extensive PCB dechlorination measured in Lake Hartwell sediments and the characterization of dechlorination end-member (EM) patterns using chemical forensic methods.

Protein from intestinal Eimeria protozoan stimulates IL-12 release from dendritic cells, exhibits antitumor properties in vivo and is correlated with low intestinal tumorigenicity.

The small intestine (SI) of vertebrates exhibits low tumorigenesis and rarely supports metastatic growth from distant tumors. Many theories have been proposed to address this phenomenon, but none has been consistently supported. One candidate mechanism is that the vast immunologic compartment of the SI provides a heightened level of tumor immunosurveillance.

Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.

Strain LB400T is the best-studied polychlorinated biphenyl (PCB) degrader. This organism has previously been allocated in the genus Burkholderia, since its 16S rRNA gene sequence shows 98.6 % sequence similarity to the type strains of Burkholderia graminis and Burkholderia terricola.

The inhibition of LPS-induced splenocyte proliferation by ortho-substituted and microbially dechlorinated polychlorinated biphenyls is associated with a decreased expression of cyclin D2.

Immunological effects of polychlorinated biphenyls (PCBs) have been demonstrated in our laboratories with the peferential inhibition of lipopolysaccharide (LPS)-induced splenocyte proliferation by ortho-substituted PCB congeners. An investigation of the mechanism behind this immunotoxicity revealed an interruption in the progression of murine lymphocytes from G0/G1 into S phase by Aroclor 1242 and the di-ortho-substituted congener, 2,2'-chlorobiphenyl (CB), whereas, a non-ortho-substituted congener, 4,4'-CB, did not affect cell cycle progression. This interruption of cell cycle progression by 2,2'-CB and Aroclor 1242 was associated with a decreased expression of the cell cycle regulatory protein, cyclin D2, while expression was not affected by exposure to the non-ortho-substituted 4,4'-CB.

Inhibition of LPS-induced splenocyte proliferation by ortho-substituted polychlorinated biphenyl congeners.

Polychlorinated biphenyls (PCBs) are persistent environmental contaminants, and their ubiquitous nature has prompted studies of their potential health hazards. As a result of their lipophilic nature, PCBs accumulate in breast milk and subsequently affect the health of offspring of exposed individuals. Biological effects of PCBs in animals have mostly been attributed to coplanar congeners, although effects of ortho congeners also have been demonstrated.

Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs.

The Gram-positive bacterium Rhodococcus sp. strain RHA1, naturally containing the biphenyl pathway, was electroporated with a broad host range plasmid containing the 4-chlorobenzoate (4-CBA) degradation operon (fcb) isolated from Arthrobacter globiformis strain KZT1. The recombinant strain grew in medium containing 4-CBA and 4-chlorobiphenyl (4-CB) as the only source of carbon, with stoichiometric release of chloride and a molar growth yield on 4-CB that suggested utilization of both biphenyl rings.