Draft Genome Sequence of a Selenite- and Tellurite-Reducing Marine Bacterium, Lysinibacillus sp. Strain ZYM-1.

Lysinibacillus sp. ZYM-1, a Gram-positive strain isolated from marine sediments, reduces selenite and tellurite efficiently. Meanwhile, it also exhibits high resistance to Zn2+ and Mn2+. Here, we report the draft genome sequence of strain ZYM-1, which contains genes related to selenite and tellurite reduction and also metal resistance.

GENOME ANNOUNCEMENT

Lysinibacillus is a Gram-positive, rod-shaped, and round-spore-forming bacterial genus in the family Bacillaceae (1). More recently, several reports have indicated that Lysinibacillus spp. are potential candidates for heavy metal bioremediation. L. fusiformis ZC1 can reduce 1 mM hexavalent chromium within 12 h, and 25 strains of L. sphaericus can grow in arsenate, hexavalent chromium, and/or lead (2, 3). Strain ZYM-1 was isolated from marine sediments using 1 mM selenite as selection pressure. This strain has been deposited in the China General Microbiological Culture Collection Center (accession number: CGMCC 1.15346). The 16S rRNA sequences of strain ZYM-1 (GenBank accession number: KT263530) revealed that it belongs to the genus Lysinibacillus. Besides the widely reported heavy metal resistance of Lysinibacillus spp., strain ZYM-1 also exhibits high selenate (MIC 10 mM), selenite (MIC 100 mM), and tellurite (MIC 2 mM) resistance. Red selenium and black tellurium nanoparticles were formed as reduction products of selenite and tellurite, which have potential application in heavy metal adsorption, photocatalysis, and energy storage (4–6). As no selenite/tellurite reduction capacity has been reported among the Lysinibacillus spp., and most strains of Lysinibacillus have been isolated from soils, the genome sequence of strain ZYM-1 may provide fundamental information of selenite/tellurite reduction genes in this species.

The genome of strain ZYM-1 was sequenced using Illumina HiSeq-2500 by PE125 strategy. The obtained reads were assembled into 84 large contigs using SOAPdenovo software (http://soap.genomics.org.cn/soapdenovo.html). Then, gene prediction was performed using the GeneMarkS server (http://opal.biology.gatech.edu). The genome sequence of ZYM-1 is 4,862,873 bp in length with G+C content of 37.86%. There are 5,006 predicted coding sequences, accounting for 85.01% of the total sequences.

A rich set of 247 annotated genes are related to inorganic ion transport and metabolism according to the COG function classification (7). As mentioned previously, strain ZYM-1 could tolerate selenite up to 10 mM, but failed to reduce this oxyanion. This is consistent with the absence of any reported genes encoding selenate reductases (serABC, srdBCA, ynfE, and ygfK) in the genome. In addition, the genes encoding NirS-type nitrite reductases are also not found (8). However, five thioredoxin reductases encoding genes are identified, which may have mediated the selenite reduction in strain ZYM-1 (9, 10). Also, two genes (dedA and cysA) encoding the possible uptake proteins selenite and selenate were found. On the other hand, we also found several genes involved in tellurite resistance and reduction, including terC, terD, yceH, and yceF (11). In addition, there are several genes involved in heavy metal resistance, such as ABC-type Mn2+/Zn2+ transport systems (ytgA, ytgB, ytgC, and ytgD) and the Zn2+ responsive regulator zur, which may relate to the Mn2+/Zn2+ resistance of strain ZYM-1. The genome sequence information indicates that strain ZYM-1 can provide a platform for selenite/tellurite detoxification and production of selenium/tellurium nanoparticles.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number LKPY00000000. The version described in this paper is the first version, LKPY01000000.