Data_Sheet_1_Metagenomics-Based Discovery of Malachite Green-Degradation Gene Families and Enzymes From Mangrove Sediment.PDF

Malachite green (MG) is an organic contaminant and the effluents with MG negatively influence the health and balance of the coastal and marine ecosystem. The diverse and abundant microbial communities inhabiting in mangroves participate actively in various ecological processes. Metagenomic sequencing from mangrove sediments was applied to excavate the resources MG-degradation genes (MDGs) and to assess the potential of their corresponding enzymes. A data set of 10 GB was assembled into 33,756 contigs and 44,743 ORFs were predicted. In the data set, 666 bacterial genera and 13 pollutant degradation pathways were found. Proteobacteria and Actinobacteria were the most dominate phyla in taxonomic assignment. A total of 44 putative MDGs were revealed and possibly derived from 30 bacterial genera, most of which belonged to the phyla of Proteobacteria and Bacteroidetes. The MDGs belonged to three gene families, including peroxidase genes (up to 93.54% of total MDGs), laccase (3.40%), and p450 (3.06%). Of the three gene families, three representatives (Mgv-rLACC, Mgv-rPOD, and Mgv-rCYP) which had lower similarities to the closest sequences in GenBank were prokaryotic expressed and their enzymes were characterized. Three recombinant proteins showed different MG-degrading activities. Mgv-rPOD had the strongest activity which decolorized 97.3% of MG (300 mg/L) within 40 min. In addition, Mgv-rPOD showed a more complete process of MG degradation compared with other two recombinant proteins according to the intermediates detected by LC-MS. Furthermore, the high MG-degrading activity was maintained at low temperature (20°C), wider pH range, and the existence of metal ions and chelating agent. Mgv-rLACC and Mgv-rCYP also removed 63.7% and 54.1% of MG (20 mg/L) within 24 h, respectively. The results could provide a broad insight into discovering abundant genetic resources and an effective strategy to access the eco-friendly way for preventing coastal pollution.</p

Number of woody plants (>1.0 m tall) ha⁻¹ in the <i>B.ablosinensis</i> stands in Qinling Mountains, China.

<p>Blanks represent no individuals found in the plot.</p

Size class distribution of the <i>B. ablosinensis</i> trees in strip clearcut and uncut <i>B. ablosinensis</i> forests of Qinling Mountains, China.

<p>Size class distribution of the <i>B. ablosinensis</i> trees in strip clearcut and uncut <i>B. ablosinensis</i> forests of Qinling Mountains, China.</p

Values of Morisita’s index (<i>I_δ</i>) for different-sized <i>B. ablosinensis</i> in 8 stands in Qinling Mountains, China.

<p>Random distribution (<i>I_δ =</i>1.0) is shown by the dot line.</p

Location of the study areas in the Qinling Mountains of China.

<p>Location of the study areas in the Qinling Mountains of China.</p

Seed removal rates of <i>P. armandii</i> and <i>Q. aliena</i> var. <i>acuteserrata</i> after deposition in the seed stations in the three experimental plots.

<p>WQ: study area located in the western Qinling Mountains; MQ: study area located in the middle Qinling Mountains; EQ: study area located in the eastern Qinling Mountains. Data are expressed as mean ± SE.</p

Characteristics of the three experimental plots.

<p>WQ: study area located in the western Qinling Mountains; MQ: study area located in the middle Qinling Mountains; EQ: study area located in the eastern Qinling Mountains.</p

Characteristics of stands and <i>B. ablosinensis</i> population in strip clearcut and uncut <i>B. ablosinensis</i> forest of Qinling Mountains.

<p>Characteristics of stands and <i>B. ablosinensis</i> population in strip clearcut and uncut <i>B. ablosinensis</i> forest of Qinling Mountains.</p

Fates of <i>P. armandii</i> seeds and <i>Q. aliena</i> var. <i>acuteserrata</i> acorns after dispersal by small rodents in the three experimental plots.

<p>WQ: study area located in the western Qinling Mountains; MQ: study area located in the middle Qinling Mountains; EQ: study area located in the eastern Qinling Mountains. IS: in situ; EIS: eaten in situ; IAR: intact after removal; EAR: eaten after removal; CAR: cached after removal; M: missing. Data are expressed as mean ± SE. **: statistically significant difference between the tree species (<i>P</i><0.01).</p

Number of small rodents captured (<i>n</i> = 150 trap days and nights) in the three experimental plots.

<p>WQ: study area located in the western Qinling Mountains; MQ: study area located in the middle Qinling Mountains; EQ: study area located in the eastern Qinling Mountains.</p