Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.
Project description:Crude oil pollution of soil is a serious environmental issue, and bioremediation using plants and microorganisms is a natural and sustainable method for its restoration. Pot incubation of a two-factor randomized block (plants with two levels, and crude oil with three levels) was designed to investigate the rhizosphere bacterial community of Suaeda salsa (L.) Pall. Crude oil contamination of soil was studied at different levels: 2 g/kg (low), 4 g/kg (medium), and 6 g/kg (high) levels. In this study, the physicochemical properties of the collected rhizosphere soil were analyzed. Moreover, the soil bacteria were further identified using the 16S rRNA gene. The effects of S. salsa and crude oil and their interaction on the physiochemical properties of the soil and crude oil degradation were found to be significant. Crude oil significantly influenced the diversity and evenness of bacteria, while the effects of S. salsa and interaction with crude oil were not significant. Proteobacteria were found to be dominant at the phylum level. Meanwhile, at the genera level, Saccharibacteria and Alcanivorax increased significantly in the low and medium contamination treatment groups with S. salsa, whereas Saccharibacteria and Desulfuromonas were prevalent in the high contamination treatment group. High crude oil contamination led to a significant decrease in the bacterial diversity in soil, while the effects of S. salsa and its interaction were not significant. Despite the highest abundance of crude oil degradation bacteria, S. salsa reduced crude oil degradation bacteria and increased bacteria related to sulfur, phosphorus, and nitrogen cycling in the low and high contamination group, whereas the opposite effect was observed for the medium contamination treatment group. The abundance of most crude oil degradation bacteria is negatively correlated with crude oil content. Nitrogen cycling bacteria are sensitive to the total nitrogen, total phosphorus, ammonia nitrogen, and nitrate nitrogen, and pH of the soil. Sulfur cycling bacteria are sensitive to aromatic hydrocarbons, saturated hydrocarbons, and asphaltene in soil. This research is helpful for further studying the mechanism of synergistic degradation by S. salsa and bacteria.
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
Project description:Carolina bays are naturally occurring shallow elliptical depressions largely fed by rain and shallow ground water. To identify members of the domain Bacteria which inhibit such an environment, we used PCR to construct a library of 16S rRNA genes (16S rDNAs) cloned from DNA extracted from the sediments of Rainbow bay, located on the Savannah River Site, near Aiken, S.C. Oligonucleotides complementary to conserved regions of 16S rDNA were used as primers for PCR, and gel-purified PCR products were cloned into vector pGEM-T. Partial sequencing of the cloned 16S rDNAs revealed an extensive amount of phylogenetic diversity within this system. Of the 35 clones sequenced, 32 were affiliated with five bacterial groups: 11 clustered with the Proteobacteria division (including members of the alpha, beta, and delta subdivisions), 8 clustered with the Acidobacterium subdivision of the Fibrobacter division (as categorized by the Ribosomal Database Project's taxonomic scheme, version 5.0), 7 clustered with the Verrucomicrobium subdivision of the Planctomyces division, 3 clustered with the gram-positive bacteria (Clostridium and relatives subdivision), and 3 clustered with the green nonsulfur bacteria. One sequence branched very deeply from the Bacteria and was found not to be associated with any of the major divisions when phylogenetic trees were constructed. Two clones did not consistently cluster with specific groups and may be chimeric sequences. None of the clones exhibited an exact match to any of the 16S rDNA sequences deposited in the databases, suggesting that most of the bacteria in Rainbow Bay are novel species. In particular, the clones related to the Acidobacterium subdivision and the Verrucomicrobium subdivision confirm the presence of novel taxa discovered previously in other molecular surveys of this type.
Project description:An anammox assay involving a ¹⁵N tracer and gas chromatography-mass spectrometry revealed that the potential anammox activity accounted for 1 to 5% of total N₂ production in a ravine paddy field, Japan. Among four 4-cm-deep layers, the top layer showed the highest activity. Clone libraries showed that the DNA in the top layer contained sequences related to those of Candidatus 'Brocadia fulgida', Ca. 'B. anammoxidans', and Ca. 'Kuenenia stuttgartiensis'. These results suggest that a specific population of anammox bacteria was present in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox.
Project description:The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia and Pseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of the Proteobacteria, and to the genus Burkholderia in particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study.
Project description:Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction A ten chip study using PCR amplicons from cloned 16S rRNA genes and from diverse soil 16S rRNAs, with PCR primers specific to the Division Acidobacteria. Each chip measures the signal from 42,194 probes (in triplicate) targeting Acidobacteria division, subdivision, and subclades as well as other bacterial phyla. All samples except one (GSM464591) include 2.5 M betaine in the hybridization buffer. Pair files lost due to a computer crash.
Project description:High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
Project description:Cemetery soils most likely contain degradative bacteria which possibly have beneficial potencies. However, the bacterial exploration in these potencies is still limitedly conducted in Indonesia. The raw sequence data of total bacteria in the cemetery soils through metagenomic analysis have been revealed. The data were obtained by collecting soil samples from six spots of two major Cemetery areas, which were Pracimaloyo (P) and Bonoloyo (B), in Surakarta City, Central Java, Indonesia. The six sample spots consisted of two samples from P area with respectively 20 cm and 140 cm depths and four samples of each two samples from B area with 20 and 40 cm depths. The total DNA was subsequently extracted from the collected soils using ZymoBIOMICS DNA Miniprep Kit. The total DNA then was amplified using a couple of 16S rRNA primers through Illumina HiSeq 2500 PE250 (Novogen, Korea) environment system. The raw sequence data has been submitted to the National Center for Biotechnology Information (NCBI) with project ID PRJNA997385. The archived sequence can be accessed in the NCBI website with the following URLs https://www.ncbi.nlm.nih.gov/sra/PRJNA997385. A brief analysis of the sequence data showed that the most common phyla in 20 cm-depths were Proteobacteria (29.5%), Actinobacteria (21.6%), and Firmicutes (19.2%), while Actinobacteria were the most found in 140 cm-depths with 34.2% followed by Proteobacteria (21.9%) and Firmicutes (16.6%). This data would be the first report of total bacterial sequence from cemetery soils in Indonesia.
Project description:Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction