The effect of different carbon sources on water quality, microbial community and structure of biofloc systems

Microorganisms play crucial roles in nutrient cycling, water quality maintenance, and farmed animal health. Increasing evidences have revealed a close association between unstable microbial environments and disease occurrences in aquaculture. Thereupon, we used high-throughput sequencing technology to comprehensively compare the bacterial communities of water, sediment, and intestine in mariculture ponds at the middle and late stages of Litopenaeus vannamei farming and analyzed whether changes of their microbiota assemblages were associated with environmental factors and shrimp physiological health. Results showed that bacterial community structures were significantly distinct among water, sediment, and intestine; meanwhile, the relative abundances of intestinal dominant taxa were significantly changed between different rearing stages. Compared with intestine and water, shrimp intestine and sediment had a similar profile of the dominant bacterial genera by cluster analysis, and the observed species, diversity indexes, and shared OTUs of bacterial communities in intestine and sediment were simultaneously increased after shrimp were farmed for 90 days. These results reflected a closer relationship between microbiotas in sediment and intestine, which was further proved by nonmetric multidimensional scaling analysis. However, bacterial communities in water, sediment, and intestine responded differently to environmental variables by redundancy and correlation analysis. More importantly, shrimp physiological parameters were closely associated with bacterial variations in the gut and/or ambient, especially the gut microbiota owning significantly high levels of predicted functional pathways involved in disease emergence. These findings may greatly add to our understanding of the microbiota characteristics of the shrimp pond ecosystem and the complex interactions among shrimp, ambient microflora, and environmental variables.

Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health

Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam.

Part I: Phylogenomics 1. Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes Christian Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards 2. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord Gergely J Szollosi and Vincent Daubin 3. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life Pere Puigbo, Yuri I. Wolf, and Eugene V. Koonin 4. Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns Eric Bapteste, Frederic Bouchard, and Richard M. Burian Part II: Natural Selection, Recombination, and Innovation in Genomic Sequences 5. Selection on the Protein Coding Genome Carolin Kosiol and Maria Anisimova 6. Methods to Detect Selection on Non-Coding DNA Ying Zhen and Peter Andolfatto 7. The Origin and Evolution of New Genes Margarida Cardoso-Moreira and Manyuan Long 8. Evolution of Protein Domain Architectures Kristoffer Forslund and Erik L.L. Sonnhammer 9. Estimating Recombination Rates from Genetic Variation in Humans Adam Auton and Gil McVean 10. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon Part III: Population Genomics 11. Association Mapping and Disease: Evolutionary Perspectives Soren Besenbacher, Thomas Mailund, and Mikkel H. Schierup 12. Ancestral Population Genomics Julien Y. Dutheil and Asger Hobolth 13. Non-Redundant Representation of Ancestral Recombinations Graphs Laxmi Parida Part IV: The "-omics" 14. Using Genomic Tools to Study Regulatory Evolution Yoav Gilad 15. Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks Gabriel Musso, Andrew Emili, and Zhaolei Zhang 16. Statistical Methods in Metabolomics Alexander Korman, Amy Oh, Alexander Raskind, and David Banks 17. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN Daniel H. Huson and Suparna Mitra 18. Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Muller, Christoph Bock, and Thomas Lengauer 19. Genetical Genomics for Evolutionary Studies Pjotr Prins, Geert Smant, and Ritsert C. Jansen Part V: Handling Genomic Data: Resources and Computation 20. Genomics Data Resources: Frameworks and Standards Mark D. Wilkinson 21. Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields, and Toshiaki Katayama 22. Scalable Computing for Evolutionary Genomics Pjotr Prins, Dominique Belhachemi, Steffen Moller, and Geert Smant

Evolutionary genomics : statistical and computational methods

Biomass is one of the most promising alternatives to petroleum-derived materials and plays a major role in fighting against global warming by providing renewable sources of chemicals and materials. Owing to its chemical and structural complexity, the transformation of biomass into value-added products requires profound understanding of its composition at different scales and using innovative methods such as combining physical and chemical processes. In this context, the use of mechanochemistry in biomass valorization is currently growing owing to its potentials as an efficient, sustainable, and environmentally friendly approach, which can facilitate biomass valorization. This review highlights the latest advances in the transformation of biomass (i.e., chitin, cellulose, hemicellulose, lignin, and starch) to functional materials using mechanochemical-assisted methods. The methodology of biomass processing, influencing factors, and resulting properties are discussed with an emphasis on achieving functional materials rather than breaking down the biopolymer chains. The opportunities and limitations associated this methodology are discussed accordingly for future directions.

Mechanochemical Transformations of Biomass into Functional Materials.

The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

/pdf/bacterial-abundance-and-diversity-in-pond-water-supplied-289pvtta1n.pdf

Bacterial abundance and diversity in pond water supplied with different feeds.

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Bacterial abundance and diversity in pond water supplied with different feeds.