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Isocitrate lyase (ICL), as the key enzyme in the glyoxylate metabolic pathway, plays an important role in metabolic adaptation to environmental changes. In this study, metagenomic DNA from the soil and water microorganism collected from the Dongzhai Harbor Mangroves (DHM) reserve, in Haikou City, China, was high-throughput sequenced using an Illumina HiSeq 4000 platform. The icl121 gene, encoding an ICL with the highly conserved catalytic pattern IENQVSDEKQCGHQD was identified. Then, this gene was subcloned into the pET-30a vector and overexpressed in Escherichia coli BL21 (DE3) cells. The maximum enzymatic activity of the recombinant ICL121 protein is 9.47 × 102 U/mg occurring at pH 7.5 and 37°C. Furthermore, as a metalo-enzyme, ICL121 can utilize the appropriate concentrations of Mg2+, Mn2+, and Na+ ion as cofactors to exhibit high enzymatic activity. In particular, the novel metagenomic-derived icl121 gene displayed distinct salt tolerance (NaCl) and might be useful for generating salt-tolerant crops in the future.

National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a “middle bridge” to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-019-00078-2) contains supplementary material, which is available to authorized users.

Acinetobacter tandoii SC36 was isolated from a mangrove wetland ecosystem in the Dongzhaigang Nature Reserve in Haikou, China. This bacterium was found to have a capacity for polyphosphate accumulation. To provide insight into its phosphorus metabolism and facilitate its application in phosphorus removal, we developed a draft genome of this strain. KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed three ppk genes and several phosphate metabolic related pathways in the genome of SC36. These genome data of Acinetobacter tandoii SC36 will facilitate elucidation of the mechanism of polyphosphate accumulation.

The mangrove ecosystem has rich biological resources and is the fourth highest service value ecosystem in the world. The Dongzhai Harbor Mangroves (DHM) reserve is located in the intertidal zone where the freshwater and seawater are dynamically interlaced, and its unique habitat may hide special microbial resources. In this study, we analyzed and compared bacterial community composition and diversity between the DHM soil and water by 16S rRNA gene sequencing and shotgun metagenomic sequencing. We found that the dominant species in both soil and water of DHM were Proteobacteria and Actinobacteria, while the most differentially abundant species were Chloroflexi and Bacteroidetes. However, shotgun metagenomic sequencing analysis identified more highly abundant species in the water than in the soil, and identified more species with significant differences between the soil and the water (P ≤ 0.0001). Network analysis identified more co-occurring species in the soil and water. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analysis identified three relatively abundant pathways: metabolism (accounting for more than 50%), genetic information processing, and environment information processing. Our results increase our understanding of bacterial community diversity in the water and soil of the DHM. Additional information that is hidden in the environment may be obtained by shotgun metagenomic sequencing; this technique can be used to mine more microbial resources from various environments.

Bacillus sp. strain QHF158, a Gram-positive, spore-forming and parasporal crystal–secreting bacterium, was isolated from soil of Limushan National Forest Park in China. Here we present the significant feature of parasporal inclusions of this organism, together with the draft genome sequence and annotation. Phylogenetic analysis suggested that strain QHF158 is possibly a novel species, most closely related to Bacillus mycoides. Genome annotation results revealed that strain QHF158 did not contain any typical Cry or Cyt toxin coding gene. Furthermore, the mass spectrometry analyses demonstrated that the parasporal crystalline inclusions were encoded by the orf_05273 gene, with 95% similarity to the S-layer protein (SLP) EA1 of B. mycoides, which indicated that the parasporal crystal from Bacillus sp. strain QHF158 was mainly formed by SLP, instead of the typical Cry or Cyt toxin proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-019-00205-z) contains supplementary material, which is available to authorized users.

The genes required for synthesis of poly (γ-glutamic acid) (γ-PGA) were cloned from Bacillus licheniformis NK-03, a strain isolated from fermented food, natto. There were three open reading frames pgsB, pgsC, pgsA in the cloned fragment, all of which were greatly similar with those from typical Bacillus subtilis strains. The alignment of deduced amino acid sequences showed that PgsC was the most conservative part in PgsBCA. Recombinant plasmid pXMJ19-PGS was constructed by a shuttle vector pXMJ19, and it was successfully transformed and expressed in the recombinant strains of Escherichia coli JM109 and Corynebacterium glutamicum ATCC13032, respectively. Expression of pgsBCA in C. glutamicum indicated that it could synthesize γ-PGA with a yield of 0.69 g/L and 97% proportion of l -glutamate monomer in the absence of glutamic acid. The results suggest that γ-PGA biosynthesis directly from glucose by genetic engineering is feasible and significant.

Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming bacteria with the ability to synthesize polysaccharides and polypeptides. Here, we report the complete genome sequence of B. amyloliquefaciens LL3, which was isolated from fermented food and presents the glutamic acid-independent production of poly-γ-glutamic acid.

A new glutamic acid independent poly-γ-glutamic acid (γ-PGA) producing strain, which was identified as Bacillus amyloliquefaciens LL3 by analysis of 16S rDNA and gyrase subunit A gene (gyrA), was isolated from fermented food. The product had a molecular weight of 470, 801 and l-glutamate monomer content of 98.47%. The pre-optimal medium, based on single-factor tests and orthogonal design, contained 50 g/L sucrose, 2g/L (NH(4))(2)SO(4), 0.6g/L MgSO(4), and provided well-balanced changes in processing parameters and a γ-PGA yield of 4.36 g/L in 200 L system. The γ-PGA synthetase genes pgsBCA were cloned from LL3, and successfully expressed by pTrcLpgs vector in Escherichia coli JM109, resulting the synthesis of γ-PGA without glutamate. This study demonstrates the designedly improved yield of γ-PGA in 200 L system and the first report of pgsBCA from glutamic acid independent strain, which will benefit the metabolized mechanism investigation and the wide-ranging application of γ-PGA.