br Data The information and results

Data The information and results presented in this data article are derived from the in vitro experiments for investigation of the arsenic responsive genes. We also provide in silico data on gene annotation that can be potentially useful for conducting microbial bioremediation of toxic metals.
Experimental design, materials and methods Lysinibacillus sphaericus B1-CDA strain was collected from a highly arsenic-contaminated region located in the south-west region of Bangladesh. Previously, we have reported that the strain L. sphaericus B1-CDA is highly resistant to arsenic and it accumulates arsenic inside the order Rocilinostat [1]. Genomic DNA was extracted from this bacterium, using Master pure™ Gram positive DNA purification kit (Epicenter, USA). Genome sequencing of the strain was performed by the Otogenetics Corporation (GA, USA). After sequencing the genome was assembled by de novo assembly employing SOAPDenovo, version 2.04 [2]. The assembled genome sequence was annotated with Rapid Annotations using Subsystems Technology, RAST [3]. Functional annotation analysis was also carried out by the Blast2GO pipeline [4] using all translated protein coding sequences resulting from the GeneMark. An InterPro scan [5] was performed through the Blast2GO interface and the InterPro IDs were merged with the Blast-derived GO-annotation for obtaining the integrated annotation results. The GO annotation of all putative metal responsive genes was manually curated. The functional annotation carried out by the RAST and Blast2GO indicates that B1-CDA contains many genes which are responsive to specific metal ions like arsenic, cobalt, copper, iron, nickel, potassium, manganese and zinc. Prediction by RAST and Blast2GO (Table 1) revealed that the B1-CDA genome contains additionally a total of 123 proteins involved in binding and transport of metal ions. Further, B1-CDA contains many other proteins (approximately 30) that catalyze binding and transport of the metal ions such as metalloendopeptidase, metalloexopeptidase, metallopeptidase, metallocarboxypeptidase and metallochaperone (Table 2). In this article, we have studied the presence of arsenic resistance genes in this bacterium by using PCR amplification. The strain B1-CDA was found to harbor acr3, arsR, arsB and arsC arsenic marker genes (Fig. 1). The arsC gene codes for the enzyme arsenate reductase, which is responsible for the biotransformation of arsenate [As(V)] to arsenite [As(III)] prior to efflux. ArsB, an integral membrane protein that pumps arsenite out of the cell, is often associated with an ATPase subunit, arsA [6]. It is hypothesized that the arsB/acr3 genes are the primary determinants in arsenite resistance [6]. The results of these studies could be used to cope with arsenic toxicity by removing it from the contaminated source or converting it to a less toxic harmless compound.
Acknowledgments This research has been funded mainly by the Swedish International Development Cooperation Agency (SIDA, Grant number: AKT-2010-018) and partly by the Nilsson-Ehle (The Royal Physiographic Society in Lund) foundation in Sweden.
Data The data composed of 56 pictures in 85,90µm depth along the Z-axis, shows the fiber matrix and cell nuclei stained with Dapi at cell density 152×106cells/mL after 34 days perfusion cultivation, taken by a fluorescence microscope.
Experimental design, materials and methods The CellTank is a perfusion-integrated Single-Use-Bioreactor (SUB), see Supplementary material 1, for a sketch of the bioreactor design. A 150cm3 cassette containing polyester non-woven spun fiber matrix, used for the cell retention, is immersed in a 2L reservoir where the perfusion of the culture medium takes place. During the culture in this system, it is not possible to take cell samples from the matrix due to the fact that the cells are entrapped in the fiber matrix. This is the reason why the cell density has been measured with an on-line biomass sensor [1]. To better understand how the cells are sitting inside the fiber matrix, the bioreactor and the cassette have been disassembled at the end of a cultivation run and the matrix scaffold has been examined by fluorescence microscopy.