2nd International Conference on Microbial Ecology & Eco Systems July 11-12, 2018 Toronto, Ontario, Canada
(10 Plenary Forums 2 days 1 event)

The focus of Baisuo Zhao research is bacterial taxonomy and microbial physiology, Molecular mechanisms of gene expression and mutagenesis. He is also interested in studies of molecular microbial ecology including the genetic and the functional diversity of microbial communities. His third research interest on Microbial Genomics & Metagenomics involves in genome analysis of pure isolates and metagenomics from extreme conditions, reactors etc.

The anaerobic haloalkaliphile Alkalitalea saponilacus SC/BZ-SP2T could utilize xylan as sole carbon source and produce propionate as the main fermentation product. The xylanase activity from A. using the combined substrates of 0.4% (w/v) sucrose + 0.1% (w/v) birch xylan was 3.2-fold than that of 0.5% (w/v) sucrose or 0.5% (w/v) birch xylan. The xylanse is halo-stable as it exhibited optimal activity at a broad range of 2-6% NaCl. Its activity was inhibited by Cu2+, Fe3+, Ni2+, Al3+, Mn2+, Co2+, Zn2+ and Ca2+ while increased 1.16-fold with the addition of Tween 20. In order to get a deep understanding of the potential genetic mechanisms of xylanase secretion and adaptive saline-alkali tolerance, the complete genome sequence of strain SC/BZ-SP2T was performed with the Pacbio SMRT and Illumina Misseq platforms. The genome contained one chromosome, with the total size of 4,775,573 bps, and the G+C content of this strain was 39.27%. A number of genes related to xylan degradation and its complete xylan degradation pathway, xyn A gene of xylanase belonging to a glycoside hydrolase (GH) family 10 and its neighborhood genes were systematically identified. Furthermore, various genes involved in biosynthesis and transportation of osmolytes, as well as genes encoding monovalent cation/proton antiporters, multi-subunit sodium/ proton antiporters, F0F1-ATP synthases, H+-transporting ATPases, Na+/solute symporters and K+ transport systems were predicted. This genome sequence provides molecular information and elucidation for halo-stable xylanase production, and will be used in the biotechnology.

Andre Freire Cruz had focused on evaluation of soil microbial status as indicator of sustainability. He has worked with many agricultural soils, recently has concentrated on fruit orchards in Japan and other countries especially concerning on analysis of microbial growth and activity. He has used many methods to evaluate the soil biology, but actually most of his researches are using metagenome analysis of bacterial and fungal genes and their relation with other soils properties.

The microbial community evaluation constitutes an essential topic to access the soil health conditions, with special regard to the operational taxonomic units (OTU). This data can easily represent the soil bacterial condition and also might distinguish many kinds of environment, such as urban areas, and agricultural soils. As a criterion to set up a “finger-print” for agricultural soils in terms of microbial community, metagenomic profiles from crops and fruit soils had their OTU analyzed after the normalizing their abundance where the sum of each sample was equivalent to 1. The bacterial and fungal genes were the target region evaluated by principal component analysis (PCA). Although some dominant taxonomic groups were constantly present in most of the soils, the OTU within the bacterial and fungal communities were specific according to the land use type (crops or fruits) i.e. each one had a remarkable difference in terms of OTU. Hokkaido prefecture contained most of specific groups, whereas other prefectures were more diverse. Similar profile was found in fungal genes. Within the bacterial genes a few number of OTUs made possible to separate crops and fruit soils, however for the fungal ones a large number was necessary for the same goal. The bacterial representative genera were Nitrospira (involved with Nitrogen cycling) and Arthrobacter. Whereas the Fusarium was the most important fungus in terms of OTU bioindicator.

Yanchun Yan has her expertise in bioremediation of environmental pollution and passion in improving the health and wellbeing. Her research team has been focused on the bioremediation for more than twenty years, and they have isolated more than 60 strains of bacteria or fungi capable of degrading pesticides or environmental estrogen chemicals. The degradation characteristics of the strains and a number of genes or gene clusters encoding key enzymes were investigated. These researches provided significant resources of strains and genes for bioremediation, and lay theoretical foundation for the degradation mechanism of pollutants.

Di-(2-ethylehxyl) phthalate (DEHP) is the most broadly representative phthalate esters (PAEs) used as a plasticizer and considered an endocrine-disrupting chemical. An efficient DEHP-degrading strain Rhodococcus ruber YC-YT1, with salt tolerance (0~12% NaCl), is the first DEHP-degrader isolated from marine plastic debris around coastal saline seawater, which could completely degraded 100 mg/L DEHP within 72 hours. Single factors (pH, temperature, and glucose) analysis and the optimum degradation conditions for the strain were measured by response surface methodology (RSM). According to HPLCMS analysis, DEHP was transformed by strain YC-YT1 into phthalate (PA) via mono (2-ethylehxyl) phthalate (MEHP), and then PA was used for cell growth. Furthermore, YC-YT1 metabolized initial concentrations of DEHP from 0.5 to 1000 mg/L. Especially, YC-YT1 degraded up to 60% of 0.5 mg/L DEHP. Moreover, compared with previous reports, strain YC-YT1 has the largest substrate spectrum, degrading up to 13 kinds of PAEs as well as diphenyl, PA, benzoic acid, protocatechuic acid (PCA), and 1,2,3,3-tetrachlorobenzene. Strain YC-YT1 could adjust its cell surface hydrophobicity (CSH) in the environment and 79.7~95.9% of DEHP-contaminated soil and water was remedied. These results demonstrate that strain YC-YT1 has vast potential to bioremediate various DEHP-contaminated environments, especially in saline environments. The whole genome sequence of strain YC-YT1 was obtained by the PacBio sequencing platform and submitted to GenBank (CP023712), which contained a circular genome and two plasmids. The genes and gene clusters involved in the degradation of PAEs and aromatic compounds, especially the phthalate dioxygenase genes and ring-cleavage dioxygenase genes, which involved the degradation of diphenyl, PCA, benzoate and phthalate were analyzed by comparative genomics analysis. Two genes (Dehp1199 and Mehp4077) encoding DEHP degrading esterases were obtained, condon optimization, expressed and verified. Dehp1199 is a novel alkaline esterase and the enzymological characteristics were analyzed.

Tetsushi Tanaka belongs to Computational Systems Biology Laboratory in Nara Institute of Science and Technology and has studied bioinformatics, especially microbiome analysis. He is also familiar with molecular biology and was graduated from Saitama University with a bachelor's degree in Science.

Microbial communities in soil depend on environmental features such as land use and geographic isolation. In this study, we have analyzed soil metagenomes sampled from a wide range in the globe and variety of land use in the context of the environment or ecosystem, from Earth Microbiome Project, containing 4998 samples and 48674 operational taxonomic units(OTUs). The final goal of this work is to discover characteristic microbiota that corresponds to land use and environment. It is worth noting that microbiome OTU data is high dimensional but sparse and many OTUs are phylogenetically related. By taking those factors into consideration, we tried to develop bioinformatics, computational methods as follows: (1) Data were labeled into 8 land use categories and applied to Random Forested to reduce variables, and we selected OTUs which relates to land use categories. (2) By using these OTUs, the differences between microbial communities were defined and clustered by UniFrac Distance which computes the distance difference based on the phylogenetic information. The results lead to the interpretation that some clusters are composed of the samples from specific areas and environments, such as cropland in Japan, montane grassland in Mongolia, tundra, and forest, and some of those clusters are characterized by different dominant OTUs, e. g. DA 101, which is known as the one of the most abundant microbial phylotypes. We have concluded that the clusters of individual lands are quite clearly reflecting the ecosystems and can be characterized by the OTUs in the microbial community.

Nancy Serrano-Silva has her expertise in molecular methods to study microbial communities in environmental samples, mainly soils and air. Currently she is a Posdoctoral Researcher in the Center of atmospheric sciences at National Autonomous University of Mexico. Serrano-Silva and Calderón-Ezquerro have been working since 3 years ago in the implementation of metagenomic to evaluation of air quality (indoor and outdoor) in Mexico City. This is one of the first jobs that report the use of equipment such as the Hirst spore trap and the Durham sampler to collect and identify the microbiota of the atmosphere by using a metagenomic focus.

Bioaerosols significantly affect atmospheric processes. The identification of airborne bacteria and fungi has traditionally been performed by retrieval in culture media, but in this way their diversity in the air is underestimated. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, so the objective of this study was to efficiently recover microorganisms from the air and standardize monitoring protocols, sample processing and molecular detection of bioaerosols of the Mexico City. To examine this bioaerosols we performed deep sequencing on the 16S rRNA and ITS genes from air samples collected during ten weeks (February to May, 2016) in south of Mexico City. Three samplers were used: a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet). A simple and efficient method for collecting bioaerosols and extracting good quality DNA for deep sequencing was standardized. The most abundant bacteria phyla in the air were Actinobacteria, Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial and fungal diversity, however it may be preferred to use one or the other sampler, as each one collected preferentially some groups, i.e. Durham favors the sampling of Cyanobacteria and HST the sampling of Firmicutes. The most abundant fungal phyla in the air were Ascomycota and Basidiomycota. Methods of sampling and processing of samples for metagenomic detection of bacteria and fungi in the air were standardized, which allows a deep exploration of the diversity of airborne bacteria and fungi.