Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill

Estimates of 7x105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of the April 20th, 2010 Deep Water Horizon drilling rig explosion, leaving thousands of square miles of earth's surface covered in crude oil. Dispersants were used on large slicks and injected at the well head, resulting in oil being suspended throughout the water column. Starting in June 2010, oil reached hundreds of miles of Louisiana, Alabama, Mississippi, and Florida shoreline disturbing the ecological balance and economic stability of the region. While visible damages are evident in the wildlife populations and marine estuaries, the most significant affect may be on the most basic level of the ecosystems: the bacterial and plankton populations.We present results from high throughput DNA sequencing of close-to-shore water and beach soil samples before and during the appearance of oil in Louisiana and Mississippi. Sixteen samples were taken over a two month period at approximately two week intervals from Grand Isle, LA and Gulfport, MS and were sequenced using the Illumina GAIIx platform. Significant genomic-based population fluctuations were observed in the soil and water samples. These included large spikes in the human pathogen Vibrio cholera, a sharp increase in Rickettsiales sp., and decrease of Synechococus sp. in water samples. Analysis of the contiguous de-novo assembled DNAs (contigs) from the samples also suggested the loss of biodiversity in water samples by the time oil appeared at the shores in both locations. Our observations lead us to the conclusion that oil strongly influenced microbial population dynamics, had a striking impact on the phytoplankton and other flora present prior to the appearance of oil, and that the microbial community had not recovered to pre-spill conditions by the end of our observational period

Microbial interactions in the mosquito gut determineSerratiacolonization and blood-feeding propensity

How microbe–microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found that, Serratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonized Aedes aegypti yet was abundant in Culex quinquefasciatus reared under identical conditions. To investigate the incompatibility between Serratia and Ae. aegypti, we characterized two distinct strains of Serratia marcescens from Cx. quinquefasciatus and examined their ability to infect Ae. aegypti. Both Serratia strains poorly infected Ae. aegypti, but when microbiome homeostasis was disrupted, the prevalence and titers of Serratia were similar to the infection in its native host. Examination of multiple genetically diverse Ae. aegypti lines found microbial interference to S. marcescens was commonplace, however, one line of Ae. aegypti was susceptible to infection. Microbiome analysis of resistant and susceptible lines indicated an inverse correlation between Enterobacteriaceae bacteria and Serratia, and experimental co-infections in a gnotobiotic system recapitulated the interference phenotype. Furthermore, we observed an effect on host behavior; Serratia exposure to Ae. aegypti disrupted their feeding behavior, and this phenotype was also reliant on interactions with their native microbiota. Our work highlights the complexity of host–microbe interactions and provides evidence that microbial interactions influence mosquito behavior

Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Background: Wolbachia , a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations.  As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium , Wolbachia  and the competing endosymbiotic bacterium Asaia . Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017.  Molecular analysis of samples was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene.  Results : Novel Wolbachia strains were discovered in five species: An. coluzzii , An. gambiae s.s., An. arabiensis , An. moucheti and An. species ‘A’, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains.  We also provide evidence for resident strain variants within An . species ‘A’.  Wolbachia is the dominant member of the microbiome in An. moucheti and An. species ‘A’, but present at lower densities in An. coluzzii .  Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were also shown to be variable and location dependent.  Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors.  Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies

Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa.

Background:  Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the  Anopheles (An.) genera, but has recently been found in  An. gambiae s.l. populations in West Africa.  As there are numerous  Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine  Wolbachia prevalence rates, characterise novel  Wolbachia strains and determine any correlation between the presence of  Plasmodium,  Wolbachia and the competing bacterium  Asaia. Methods:  Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017.  Molecular analysis was undertaken using quantitative PCR, Sanger sequencing,  Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial  16S rRNA gene.  Results: Novel  Wolbachia strains were discovered in five species:  An. coluzzii,  An. gambiae s.s.,  An. arabiensis,  An. moucheti and  An. species A, increasing the number of  Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with  Wolbachia supergroup B strains.  We also provide evidence for resident strain variants within  An. species A.  Wolbachia is the dominant member of the microbiome in  An. moucheti and  An. species A but present at lower densities in  An. coluzzii.  Interestingly, no evidence of  Wolbachia/Asaia co-infections was seen and  Asaia infection densities were shown to be variable and location dependent.  Conclusions: The important discovery of novel  Wolbachia strains in  Anopheles provides greater insight into the prevalence of resident  Wolbachia strains in diverse malaria vectors.  Novel  Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other  Anopheles mosquito species, which could be used for population replacement or suppression control strategies

The Estimation of the Stability of Plants Constituting the Photosynthesizing Unit of Bioregenerative Life Support Systems for Including Them into the Plant Waste Mass Exchange

One of the ways of increasing the closure of mass exchange processes in the bioregenerative life support systems (BLSS) may be the technology of plant cultivation on the so-called soil-like substrate (SLS) which is expected to utilize inedible plant biomass with the help of the SLS heterotrophic link. Earlier, based on the example of the radish inedible biomass, there was shown the principal possibility of its successful biological combustion (without decreasing the productivity of the plants cultivated) during their direct introduction into the SLS. The possibility of a direct plant waste introduction into the SLS could considerably simplify the technological processes of their biological combustion and increase their efficiency. However, there were no experiments carried out with respect to the other vegetables included into the BLSS photosynthesizing link. The aim of the given work is estimating the possible influence of the inedible biomass of different plant species introduced into the SLS, on the plant productivity. Several series of the test experiments were carried out. In the first experiment series, dried radish leafy tops making up 0.8 kg/m2 of the sown area, dried carrot leafy tops – 3.1 kg/m2 and dried beet leafy tops – 2.5 kg/m2 were introduced into the SLS makeup. As a test culture, there was taken the radish Raphanus sativus L of the Virovsky Beliy species. In the second experiment series, before the sowing of radish and wheat, there were introduced 1.2 kg/m2 and 3.1 kg/m2 of dry wheat straw into the SLS respectively. In the third series of the experiments, the wheat straw, before being introduced into the SLS, was subjected to the preliminary processing. In the fourth experiment series, there was studied the supposition about the possibility of decreasing the negative influence of introducing the vegetable tops into the SLS on the plant growth of the succeeding generation under the conditions of growing plants on a various-ages multi-species vegetable conveyor. According to the results of the research, the direct introduction of carrot and beet tops, as well as dry wheat straw, resulted in the considerable drop of the plant productivity. The vegetable cultivation in a conveyor mode done for three generations, also resulted in their productivity decrease. It was shown that the straw mineralization by using the method of “wet incineration” developed by Yu. A. Kudenko had completely removed the negative effect of the plant waste on the plant growth and could be the alternative way of the wheat waste utilization

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations

The Estimation of the Stability of Plants Constituting the Photosynthesizing Unit of Bioregenerative Life Support Systems for Including Them into the Plant Waste Mass Exchange

One of the ways of increasing the closure of mass exchange processes in the bioregenerative life support systems (BLSS) may be the technology of plant cultivation on the so-called soil-like substrate (SLS) which is expected to utilize inedible plant biomass with the help of the SLS heterotrophic link. Earlier, based on the example of the radish inedible biomass, there was shown the principal possibility of its successful biological combustion (without decreasing the productivity of the plants cultivated) during their direct introduction into the SLS. The possibility of a direct plant waste introduction into the SLS could considerably simplify the technological processes of their biological combustion and increase their efficiency. However, there were no experiments carried out with respect to the other vegetables included into the BLSS photosynthesizing link. The aim of the given work is estimating the possible influence of the inedible biomass of different plant species introduced into the SLS, on the plant productivity. Several series of the test experiments were carried out. In the first experiment series, dried radish leafy tops making up 0.8 kg/m2 of the sown area, dried carrot leafy tops – 3.1 kg/m2 and dried beet leafy tops – 2.5 kg/m2 were introduced into the SLS makeup. As a test culture, there was taken the radish Raphanus sativus L of the Virovsky Beliy species. In the second experiment series, before the sowing of radish and wheat, there were introduced 1.2 kg/m2 and 3.1 kg/m2 of dry wheat straw into the SLS respectively. In the third series of the experiments, the wheat straw, before being introduced into the SLS, was subjected to the preliminary processing. In the fourth experiment series, there was studied the supposition about the possibility of decreasing the negative influence of introducing the vegetable tops into the SLS on the plant growth of the succeeding generation under the conditions of growing plants on a various-ages multi-species vegetable conveyor. According to the results of the research, the direct introduction of carrot and beet tops, as well as dry wheat straw, resulted in the considerable drop of the plant productivity. The vegetable cultivation in a conveyor mode done for three generations, also resulted in their productivity decrease. It was shown that the straw mineralization by using the method of “wet incineration” developed by Yu. A. Kudenko had completely removed the negative effect of the plant waste on the plant growth and could be the alternative way of the wheat waste utilization

<it>Slim-Filter</it>: an interactive windows-based application for illumina genome analyzer data assessment and manipulation

Abstract Background The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data is limited due to large file sizes, so even simple tasks such as data filtration and quality assessment have to be performed in several steps. This requires (potentially problematic) interaction between the investigator and a bioinformatics/computational service provider. Furthermore, such services are often performed using specialized computational facilities. Results We present a Windows-based application, Slim-Filter designed to interactively examine the statistical properties of sequencing reads produced by Illumina Genome Analyzer and to perform a broad spectrum of data manipulation tasks including: filtration of low quality and low complexity reads; filtration of reads containing undesired subsequences (such as parts of adapters and PCR primers used during the sample and sequencing libraries preparation steps); excluding duplicated reads (while keeping each read’s copy number information in a specialized data format); and sorting reads by copy numbers allowing for easy access and manual editing of the resulting files. Slim-Filter is organized as a sequence of windows summarizing the statistical properties of the reads. Each data manipulation step has roll-back abilities, allowing for return to previous steps of the data analysis process. Slim-Filter is written in C++ and is compatible with fasta, fastq, and specialized AS file formats presented in this manuscript. Setup files and a user’s manual are available for download at the supplementary web site (https://www.bioinfo.uh.edu/Slim_Filter/). Conclusion The presented Windows-based application has been developed with the goal of providing individual investigators with integrated sequencing reads analysis, curation, and manipulation capabilities.</p