Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline

Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment

Diversity of bacterial communities in acid mine drainage from the Shen-bu copper mine, Gansu province, China

This study presents bacterial population analyses of microbial communities inhabiting three sites of acid mine drainage (AMD) in the Shen-bu copper mine, Gansu Province, China. These sites were located next to acid-leached chalcopyrite slagheaps that had been abandoned since 1995. The pH values of these samples with high concentrations of metals ranged from 2.0 to 3.5. Amplified ribosomal DNA restriction analysis (ARDRA) was used to characterize the bacterial population by amplifying the 16S rRNA gene of microorganisms. A total of 39 operational taxonomic units (OTUs) were obtained from the three samples and sequenced from 384 clones. Sequence data and phylogenetic analyses showed that two dominant clones (JYC-1B, JYC-1D) in sample JYC-1 represented 69.5% of the total clones affiliated with Acidithiobacillus ferrooxidans (\u3b3-Proteobacteria), and the most dominant clones of JYC-2 and JYC-3 were affiliated with Caulobacter crescentus (\u3b1-Protebacteria). At the level of bacterial divisions, differences in the relative incidence of particular phylogenetic groups among the three samples and discrepancies in physicochemical characteristics suggested that the physico-chemical characteristics had an influence on phylogenetic diversity. Furthermore, the relationships between the discrepancies of physicochemical characteristics and the diversity of the bacteria communities in the three samples suggested that the biogeochemical properties, pH and concentration of soluble metal, could be key factors in controlling the structure of the bacterial population

Effects of experimental warming and clipping on metabolic change of microbial community in a US Great Plains tallgrass prairie

While more and more studies are being conducted on the effects of global warming, little is known regarding the response of metabolic change of whole soil microbial communities to this phenomenon. In this study, functional gene changes at the mRNA level were analyzed by our new developed GeoChip 3.0. Soil samples were taken from a long-term climate warming experiment site, which has been conducted for ~;;8 years at the Kessler Farm Field Laboratory, a 137.6-ha farm located in the Central Redbed Plains, in McClain County, Oklahoma. The experiment uses a paired factorial design with warming as the primary factor nested with clipping as a secondary factor. An infrared heater was used to simulate global warming, and clipping was used to mimic mowing hay. Twelve 2m x 2m plots were divided into six pairs of warmed and control plots. The heater generates a constant output of ~;;100 Watts m-2 to approximately 2 oC increase in soil temperature above the ambient plots, which is at the low range of the projected climate warming by IPCC. Soil whole microbial communities? mRNA was extracted, amplified, labeled and hybridized with our GeoChip 3.0, a functional gene array covering genes involved in N, C, P, and S cycling, metal resistance and contaminant degradation, to examine expressed genes. The results showed that a greater number and higher diversity of genes were expressed under warmed plots compared to control. Detrended correspondence analysis (DCA) of all detected genes showed that the soil microbial communities were clearly altered by warming, with or without clipping. The dissimilarity of the communities based on functional genes was tested and results showed that warming and control communities were significantly different (P<0.05), with or without clipping. Most genes involved in C, N, P and S cycling were expressed at higher levels in warming samples compared to control samples. All of the results demonstrated that the whole microbial communities increase functional gene expression under warming with or without clipping in order to adapt the changed out environment. More detail analysis is underway

Climate warming accelerates temporal scaling of grassland soil microbial biodiversity.

Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges

Recent Progress in Electric Furnace Titanium Slag Processing and Utilization: A Review

Titanium slags produced through ilmenite electric furnace smelting contain 60–80%TiO2, a vital titanium resource in the titanium industry. The processing and utilization of titanium slag is faced with many challenges, such as complex mineral structures, high requirements, severe environmental pollution, and heavy additives and energy consumption. This study aims to review the technologies for the processing and utilization of titanium slag. First, we analyze the characteristics of titanium slag from different regions. Then, we discuss in detail the methods for processing and using titanium slag. The progress in electric furnace titanium slag processing and utilization can be divided into two areas: the preparation of titanium dioxide and high-quality titanium-rich materials. These include H2SO4 leaching, HCl leaching, fluoride leaching, sulfur roasting–leaching, alkaline roasting–leaching, oxide roasting–leaching, oxidation and reduction roasting–leaching, phosphorylation roasting–leaching, and ammonia decomposition leaching. Further development of oxide roasting–leaching for the extraction of titanium from titanium slag is recommended

Recent Progress in Electric Furnace Titanium Slag Processing and Utilization: A Review

Titanium slags produced through ilmenite electric furnace smelting contain 60–80%TiO2, a vital titanium resource in the titanium industry. The processing and utilization of titanium slag is faced with many challenges, such as complex mineral structures, high requirements, severe environmental pollution, and heavy additives and energy consumption. This study aims to review the technologies for the processing and utilization of titanium slag. First, we analyze the characteristics of titanium slag from different regions. Then, we discuss in detail the methods for processing and using titanium slag. The progress in electric furnace titanium slag processing and utilization can be divided into two areas: the preparation of titanium dioxide and high-quality titanium-rich materials. These include H2SO4 leaching, HCl leaching, fluoride leaching, sulfur roasting–leaching, alkaline roasting–leaching, oxide roasting–leaching, oxidation and reduction roasting–leaching, phosphorylation roasting–leaching, and ammonia decomposition leaching. Further development of oxide roasting–leaching for the extraction of titanium from titanium slag is recommended

Column bioleaching of low-grade copper ore by Acidithiobacillus ferrooxidans in pure and mixed cultures with a heterotrophic acidophile Acidiphilium sp.

The aim of this investigation was to compare a pure culture of Acidithiobacillus ferrooxidans GF with a mixed culture with Acidiphilium sp. DX1-1 in the bioleaching of low-grade copper ore. The leaching experiments were carried out at ambient temperature. The influence of temperature, pH, redox potential and concentration of total iron and ferric ion in solution on the performance of column bioleaching was also investigated. Total DNA was extracted from the mineral samples taken at different depths from the column top surface, and the corresponding microbial community structures were examined using amplified ribosomal DNA restriction analysis (ARDRA). Copper extractions by the pure and mixed cultures achieved 14.87% and 20.11% respectively over a period of 117 days, including 15 days of acid pre-leaching and 102 days of bioleaching. The ratios between autotrophic and heterotrophic bacteria at the top and bottom portions of the columns were 1.20:1 and 2.14:1, respectively. (C) 2012 Elsevier B.V. All rights reserved