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.

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.

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.

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.

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.

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.

Dechlorination of Four Commercial Polychlorinated Biphenyl Mixtures (Aroclors) by Anaerobic Microorganisms from Sediments.

The rate, extent, and pattern of dechlorination of four Aroclors by inocula prepared from two polychlorinated biphenyl (PCB)-contaminated sediments were compared. The four mixtures used, Aroclors 1242, 1248, 1254, and 1260, average approximately three, four, five, and six chlorines, respectively, per biphenyl molecule. All four Aroclors were dechlorinated with the loss of meta plus para chlorines ranging from 15 to 85%.