Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test H. utahensis growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects

Enhancing biogas production by anaerobic codigestion of water hyacinth and pig manure

The characteristics of anaerobic batch co-digestion of water hyacinth (WH) with pig manure (PM) under seven mixing ratio 100%WH; 80%WH : 20%PM; 60%WH : 40%PM; 50%WH : 50%PM; 40%WH : 60%PM; 20%WH : 80%PM and 100%PM were investigated, each treatment was conducted in five replications with daily loading rate at 1 gVS.L-1.day-1. During the anaerobic digestion process of 60 days, maximum biogas production occurred in two periods, the first stage from 12- 22 days and second stage from 30 - 35 days. The maximum daily biogas productions from each stage were 17.2 L.day-1 and 15.1 L.day-1, respectively. The cumulative biogas production varied between 60 L (100%PM) and 360 L (60%WH : 40%PM). The results showed that the biogas yields of co-digestion 40- 80%WH were higher from 34.6 to 56.1% in comparison with 100%PM and from 109 to 143% in comparison with 100%WH. When mixing with WH, treatments were received more methane and the methane contents were higher than 45% (v/v) that good for energy using purposes.Nghiên cứu được thực hiện nhằm khảo sát khả năng gia tăng lượng khí sinh học khi tiến hành đồng phân hủy yếm khí lục bình (WH) và phân heo (PM) ở các tỉ lệ phối trộn khác nhau gồm 100%WH; 80%WH : 20%PM; 60%WH : 40%PM; 50%WH : 50%PM; 40%WH : 60%PM; 20%WH : 80%PM và 100%PM. Các nghiệm thức được nạp lượng nguyên liệu là 1 gVS.L-1.ngày-1 và bố trí lặp lại 5 lần. Theo dõi quá trình phân hủy của các nghiệm thức trong 60 ngày ghi nhận có 2 khoảng thời gian lượng khí sản sinh nhiều nhất - giai đoạn 1 từ ngày 12 đến 22, giai đoạn 2 từ ngày 30 đến 35. Lượng khí sản sinh cao nhất tương ứng trong mỗi giai đoạn là 17.2 L.ngày-1 và 15.1 L.ngày-1. Lượng khí tích lũy trong suốt thời gian thí nghiệm ghi nhận thấp nhất ở nghiệm thức 100%PM đạt 60 L, và cao nhất ở nghiệm thức 60%WH : 40%PM đạt 360 L. Năng suất khí sinh ra của các nghiệm thức phối trộn lục bình từ 40 đến 80% cao hơn từ 34,6 đến 56,1% so với nghiệm thức 100%PM và cao hơn từ 109% đến 143% so với nghiệm thức 100%WH. Hàm lượng mê-tan sinh ra từ các nghiệm thức có phối trộn lục bình ổn định trong khoảng > 45% đảm bảo nhiệt lượng cho nhu cầu sử dụng năng lượng

Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake

This article is free to read on the publishers website A new halophilic sulfate-reducing bacterium, strain GSL-But2T, was isolated from surface sediment of the Southern arm of the Great Salt Lake, UT, USA. organism grew with a number of straight-chain fatty acids (C4-C16), 2-methylbutyrate, L-alanine and pyruvate as electron donors. Butyrate was oxidized incompletely to acetate. Sulfate, but not sulfite or thiosulfate, serv as an electron acceptor. Growth was observed between 2 and 19% (w/v) NaCl with an optimum at 4-5% (w/v) NaCl. The optimal temperature and pH for growth were around 34°C and pH 6.5-7.3, respectively. The generation time under optimal conditions in defined medium was around 28 h, compared to 20 h in complex medium containing yeast extract. The G+C content was 35.0 mol%. 16S rRNA gene sequence analysis revealed that strain GSL-But2Tbelongs to the family Desulfobacteriaceae within the delta-subclass of the Proteobacteria and suggested that strain GSL-But2Trepresents a member of new genus. The name Desulfocella halophila gen. nov., sp. nov. is proposed for this organism. The type strain of D. halophila is strain GSL-But2T(= DSM 117 = ATCC 700426T)