Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

https://www.cell.com/trends/neurosciences/pdf/S0166-2236(08)00132-X.pdf

White matter in learning, cognition and psychiatric disorders.

A review on heavy metal pollution, toxicity and remedial measures: Current trends and future perspectives

A field experiment was conducted in Delaware (USA) to evaluate three crude oil bioremediation techniques. Four treatments were studied: no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum. The microbial populations were monitored by standard MPN techniques, PLFA profile analysis, and 16S rDNA DGGE analysis for species definition. Viable MPN estimates showed high but steadily declining microbial numbers and no significant differences among treatments during the 14-weeks. Regarding the PLFA results, the communities shifted over the 14-week period from being composed primarily of eukaryotes to Gram-negative bacteria. The Gram-negative communities shifted from the exponential to the stationary phase of growth after week 0. All Gram-negative communities showed evidence of environmental stress. The 16S rDNA DGGE profile of all plots revealed eight prominent bands at time zero. The untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. The original banding pattern disappeared rapidly in all oiled plots, indicating that the dominant species diversity changed and increased substantially over 14 weeks. The nature of this change was altered by nutrient-addition and the addition of the indigenous inoculum.

/pdf/microbial-population-changes-during-bioremediation-of-an-46czbde8f8.pdf

Microbial Population Changes During Bioremediation of an Experimental Oil Spill

The exploration of renewable, cost-effective, and environmentally friendly electrode materials with high adsorption, fast ion/electron transport, and tunable surface chemistry is urgently needed for the development of next-generation biocompatible energy-storage devices. In recent years, biomass-derived carbon electrode materials for energy storage have attracted significant attention because of their widespread availability, renewable nature, and low cost. More importantly, their inherent uniform and precise biological structures can be utilized as templates for fabricating electrode materials with controlled and well-defined geometries. Meanwhile, the basic elements of biomass are carbon, sulfur, nitrogen, and phosphorus. The special naturally ordered hierarchical structures as well as abundant surface properties of biomass-derived carbon materials are compatible with electrochemical reaction processes such as ion transfer and diffusion. To date, a series of novel porous carbon materials with different dimensions have been prepared by various methods using biomass as the raw material, which is an important field in the fabrication of supercapacitor electrode materials. Herein, we summarized recently reported biomass-derived carbon materials with one-dimensional, two-dimensional, and three-dimensional structures and their applications as carbon-based electrode materials for supercapacitors. Finally, the current challenges and future perspectives of the carbon-based electrode materials with respect to the supercapacitor's performance were closely highlighted.

Biomass-derived porous carbon materials with different dimensions for supercapacitor electrodes: a review

Objective: To detect white matter abnormalities in patients with mild Alzheimer disease ( AD) by diffusion tensor imaging and to determine their topographic relationship with gray matter atrophy. Methods: Thirteen patients with mild AD and 16 normal age-matched volunteers underwent diffusion tensor imaging and three-dimensional spoiled gradient-recalled sequence scanning. Voxel-based morphometry was conducted to detect regions of gray matter atrophy in the AD group relative to the control group. Fractional anisotropy (FA) maps were processed using SPM2 to make voxel-wise comparison of anisotropy in whole brain between the two groups. The relationship between locations of abnormalities in the white and gray matter was examined. Results: Significant reductions in anisotropy were found in the white matter of both medial temporal lobes, bilateral temporal stems, bilateral superior longitudinal fasciculi, bilateral internal capsules, and cerebral peduncles, as well as the white matter of left middle temporal gyrus and right superior parietal lobule, the body and genu of the corpus callosum, and the right lateral capsule in patients with AD. Although the decrease in FA was consistent with cortical volumetric reduction in both temporal lobes, the widespread involvement of bilateral superior longitudinal fasciculi was dominant in these white matter findings. Conclusions: Voxel-wise comparison of whole-brain anisotropy revealed widely distributed disintegration of white matter in mild Alzheimer disease (AD). The white matter shows a different pattern of degeneration from gray matter and may be an independent factor in the progress of AD.

Voxel-based detection of white matter abnormalities in mild Alzheimer disease

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes.

Antibiotic ciprofloxacin is ubiquitous in the environment. However, little is known about ciprofloxacin dissipation by microbial community. The present study investigated the biodegradation potential of ciprofloxacin by mixed culture and the influential factors and depicted the structure of ciprofloxacin-degrading microbial community. Both the original microbiota from drinking water biofilter and the microbiota previously acclimated to high levels of ciprofloxacin could utilize ciprofloxacin as sole carbon and nitrogen sources, while the acclimated microbiota had a much stronger removal capacity. Temperature rise and the presence of carbon or nitrogen sources favored ciprofloxacin biodegradation. Many novel biotransformation products were identified, and four different metabolic pathways for ciprofloxacin were proposed. Bacterial community structure illustrated a profound shift with ciprofloxacin biodegradation. The ciprofloxacin-degrading bacterial community was mainly composed of classes Gammaproteobacteria, Bacteroidia, and Betaproteobacteria. Microorganisms from genera Pseudoxanthomonas, Stenotrophomonas, Phenylobacterium, and Leucobacter might have links with the dissipation of ciprofloxacin. This work can provide some new insights towards ciprofloxacin biodegradation.

Shuguang Xie

Papers

Voxel-based detection of white matter abnormalities in mild Alzheimer disease

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes.

Biodegradation of antibiotic ciprofloxacin: pathways, influential factors, and bacterial community structure.

Overview of sulfonamide biodegradation and the relevant pathways and microorganisms.

Changes of biomass and bacterial communities in biological activated carbon filters for drinking water treatment