Project description:In aquatic environments, the production and consumption of organic compounds is directly tied to the metabolic potential of the in situ microbial community. The community’s metabolic potential can be assessed using metatranscriptomics, which is a measure of gene expression in the environment. More recently, advances in metabolomics deliver details on specific organic compounds found in the environment. While the integration of these two datasets is desirable, the vast data streams can hinder investigations into biological and chemical processes. Here, we use data in the Kyoto Encyclopedia of Genes and Genomes (KEGG) combined with K means clustering to jointly interrogate metabolomics and metatranscriptomics data collected from a coastal marine environment. Using KEGG allowed us to focus our analysis on genes and compounds connected by a defined biochemical reaction. The K means clustering provided an unbiased means to place metabolites and genes into groups based on their temporal variability. Each of the groups defined by the K means clustering contained both transcripts and metabolites, which emphasized the interconnected nature of these two datasets. While conceptually simple, this analysis allowed us to explore a tractable number of biochemical pathways within our data. Continued development of computational tools to analyze meta-omics data is a pressing need. The application of tools such as described here is an exciting step towards integrated multi-omics data analysis that can be used to address broad questions in biogeochemical cycling.
Project description:BackgroundCoral reefs worldwide are being harmed through anthropogenic activities. Some coral reefs in Thailand remain well-preserved, including the shallow coral reefs along Kra island, Nakhon Si Thammarat province. Interestingly, the microbial community in this environment remains unknown. The present study identified biodiversity of prokaryotes and eukaryotes of 0.22-30 μm in sizes and their metabolic potentials in this coral reef surface in summer and winter seasons, using 16S and 18S rRNA genes pyrosequencing.ResultsThe marine microbial profiles in summer and winter seasons comprised mainly of bacteria, in phylum, particular the Proteobacteria. Yet, different bacterial and eukaryotic structures existed between summer and winter seasons, supported by low Lennon and Yue & Clayton theta similarity indices (8.48-10.43% for 16S rRNA, 0.32-7.81% for 18S rRNA ). The topmost prokaryotic phylum for the summer was Proteobacteria (99.68%), while for the winter Proteobacteria (62.49%) and Bacteroidetes (35.88%) were the most prevalent. Uncultured bacteria in phyla Cyanobacteria, Planctomycetes, SAR406 and SBR1093 were absent in the summer. For eukaryotic profiles, species belonging to animals predominated in the summer, correlating with high animal activities in the summer, whereas dormancy and sporulation predominated in the winter. For the winter, eukaryotic plant species predominated and several diverse species were detected. Moreover, comparison of our prokaryotic databases in summer and winter of Kra reef surface against worldwide marine culture-independent prokaryotic databases indicated our databases to most resemblance those of coastal Sichang island, Chonburi province, Thailand, and the 3 tropical GOS sites close to Galapagos island (GS039, GS040 and GS045), in orderly.ConclusionsThe study investigated and obtained culture-independent databases for marine prokaryotes and eukaryotes in summer and winter seasons of Kra reef surface. The data helped understand seasonal dynamics of microbial structures and metabolic potentials of this tropical ecosystem, supporting the knowledge of the world marine microbial biodiversity.
Project description:Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world's oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.
Project description:Scrub typhus, a rickettsial disease caused by Orientia spp., is transmitted by infected larval trombiculid mites (chiggers). We report the molecular detection of Orientia species in free-living Eutrombicula chiggers collected in an area in North Carolina, USA, to which spotted fever group rickettsiae infections are endemic.
Project description:We have determined optical properties of heterogeneous particles from aerosol samples collected at Hawaii's Mauna Loa Observatory. Back trajectories, satellite imagery, and composition differences among particles from scanning electron microscopy revealed a subset of particles with dolomite or calcite that likely came from Asia. Using focused ion-beam tomography and the discrete dipole approximation, we show how small amounts of an iron phase (oxide or carbonate), or in one case soot, affected extinction and scattering compared with particles of neat dolomite or calcite. We show how particles exhibit a range scattering values due to varying orientations of the inclusion phases. Extinction efficiencies for the heterogeneous particles with dolomite (3.47) and calcite (3.36) were 19% to 21% lower than extinction for marine background air particles (3.72). Extinction for the Asian dust was, however, generally higher than for the neat particles. Compared to iron carbonate, the presence of an absorbing iron oxide affected scattering in Asian dust particles even at the low oxide concentrations studied here (0.6% to 8.1%). Scattering efficiency decreased by <1% with a 1% increase in hematite but by 2% to 5% with magnetite. Asian dust scattered light strongly forward, but backscattering was 56% larger than for the marine background air particles. Backscattering in the Asian dust was also larger with magnetite than hematite. Single scattering albedo for Asian dust with hematite, magnetite, or soot averaged 0.96 ± 0.06 (x¯±s,n=19) but was as low as 0.72 with a magnetite mass of 5.8%.
Project description:Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the ribosomal RNA (rRNA) gene cluster, a fragment of the translation elongation factor 1-alpha (tef1) gene, and random amplified polymorphic DNA (RAPD) markers were applied to determine the genetic diversity of Trichoderma atroviride strains collected in Poland, and also in order to identify loci and PCR-based molecular markers useful in genetic variation assessment of that fungus. Although tef1 and RAPD analysis showed limited genetic diversity among T. atroviride strains collected in Poland, it was possible to distinguish major groups that clustered most of the analyzed strains. Polymorphic RAPD amplicons were cloned and sequenced, yielding sequences representing 13 T. atroviride loci. Based on these sequences, a set of PCR-based markers specific to T. atroviride was developed and examined. Three cleaved amplified polymorphic sequence (CAPS) markers could assist in distinguishing T. atroviride strains. The genomic regions identified may be useful for further exploration and development of more precise markers suitable for T. atroviride identification and monitoring, especially in environmental samples.
Project description:Despite stringent biosecurity measures, infections by bacterial food pathogens such as Campylobacter are a recurrent problem in industrial poultry houses. As the main transmission route remains unclear, persistence of these infections has been linked to bacterial survival and possibly multiplication within protozoan vectors. To date, however, virtually no information is available on the diversity and occurrence of free-living protozoa in these environments. Using a combination of microscopic analyses of enrichment cultures and molecular methods (denaturing gradient gel electrophoresis [DGGE]) on natural samples, we show that, despite strict hygiene management, free-living protozoa are common and widespread throughout a 6-week rearing period in both water and dry samples from commercial poultry houses. Protozoan communities were highly diverse (over 90 morphotaxa and 22 unique phylotypes from sequenced bands) and included several facultative pathogens and known bacterial vectors. Water samples were consistently more diverse than dry ones and harbored different communities, mainly dominated by flagellates. The morphology-based and molecular methods yielded markedly different results: amoebic and, to a lesser degree, ciliate diversity was seriously underestimated in the DGGE analyses, while some flagellate groups were not found in the microscopic analyses. Some recommendations for improving biosecurity measures in commercial poultry houses are suggested.