Mycoplanktonic Community Structure and Their Roles in Monitoring Environmental Changes in a Subtropical Estuary in the Beibu Gulf

Mycoplankton are an important component of marine ecosystems and play a key role in material cycling and energy flow in marine ecosystems. In this study, high-throughput sequencing of the 18S rDNA gene was employed to investigate the community structure of mycoplankton during summer and winter and their response to environmental changes in the Dafengjiang River estuary in the Beibu Gulf, Guangxi. The mycoplanktonic community was generally dominated by Ascomycota, Basidiomycota, and Cryptomycota. However, there were significant seasonal differences in the α-diversity of the mycoplanktonic community (p < 0.05). Random forest modeling also revealed that Paramicrosporidium, Parengyodontium, Arthrinium, Paramycosphaerella, Pestalotia, and Talaromyces were the most effective bioindicators of environmental changes. Spearman’s correlation analysis and distance-based redundancy analysis suggested that the trophic status, chemical oxygen demand, dissolved oxygen, and salinity were the key environmental factors regulating the mycoplanktonic community structure. Variation partitioning analysis also found that nutrient levels were the main driver of the β-diversity of the mycoplanktonic community, showing a greater effect than the water quality parameters. In conclusion, this study revealed the mycoplanktonic community structure and its key drivers in the Dafengjiang River estuary, thus providing a theoretical reference for ecological environmental monitoring and resource management in the Beibu Gulf

Effects of environmental factors on mycoplankton diversity and trophic modes in coastal surface water

Mycoplankton play a key role in aquatic microbial food webs and nutrient cycling. However, the environmental factors that affect their composition and trophic modes in coastal water remain unclear. In this study, we used fungal metabarcoding to characterize seasonal mycoplanktonic communities in the surface water of the Maowei Sea. Dothideomycetes and Sordariomycetes were the dominant classes in the Maowei Sea. Random forest modeling analyses suggested that Ochroconis, Rhodotorula, Perenniporia and Derxomyces were the best seasonal bioindicators of environmental changes. Spearman’s correlation analysis showed that TOC (total organic carbon) is the main factor affecting mycoplanktonic bioindicators. Through FUNGuild analysis, we classified mycoplankton in the Maowei Sea into eight trophic modes and found that saprotrophs were the most abundant. Random forest analysis and Spearman’s correlation indicated that the mycoplankton trophic modes could reflect environmental changes in the Maowei Sea and were mainly influenced by dissolved inorganic phosphorus (DIP), dissolved oxygen (DO), and total organic carbon (TOC). Mycoplanktonic alpha and beta diversities significantly varied in different seasons (p < 0.05). Spearman rank’s test, Mantel test, and partial Mantel test indicated that TOC was the key environmental factor that affected the mycoplanktonic alpha and beta diversities. Variation partition analysis revealed that mycoplankton community structure was affected more due to nutrient variability than water quality (18 % vs 7 %). Overall, this study enhanced our understanding of the key controlling environmental factors affecting mycoplanktonic diversities and trophic modes in the coastal environment

Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms

<div><p>L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named <i>ldc1E</i> was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5′-phosphate. The <i>ldc1E</i> gene was subcloned into the pET-30a(+) vector and highly expressed in <i>Escherichia coli</i> BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent <i>K</i>_m, <i>k</i>_cat, and <i>k</i>_cat/<i>K</i>_m values of 1.08±0.16 mM, 5.09±0.63 s⁻¹, and 4.73×10³ s⁻¹ M⁻¹, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg⁻¹ protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.</p></div

RP-HPLC profile of the reaction product from the decarboxylation of L-lysine HCl substrate under Ldc1E catalysis.

<p>The enzymatic product was derivatized with dansyl chloride.</p

Effects of temperature and pH on the activity and stability of Ldc1E.

<p>(A) Optimum reaction temperature of the recombinant Ldc1E. The enzyme activity was measured at various temperatures from 20°C to 60°C with 5°C intervals in 0.2 M Na₂HPO₄/0.1 M citric acid buffer (pH 6.5). Relative activity of 100% represents the specific activity of 1.50±0.06 U mg⁻¹ protein. (B) Effect of temperature on the enzymatic activity of recombinant Ldc1E. Relative activity of 100% represents the specific activity of 1.53±0.06 U mg⁻¹ protein. (C) Effect of pH on the enzymatic activity of recombinant Ldc1E. The enzyme activity was measured in 0.2 M Na₂HPO₄/0.1 M citric acid (4.0–8.0) and 0.1 M glycine–NaOH (8.0–10.0) at 40°C. Relative activity of 100% represents the specific activity of 1.53±0.06 U mg⁻¹ protein. (D) Effect of stable pH on the enzymatic activity of the recombinant Ldc1E. Relative activity of 100% represents the specific activity of 0.93±0.05 U mg⁻¹ protein.</p

Properties of L-lysine decarboxylase from various sources.

<p>Properties of L-lysine decarboxylase from various sources.</p

Homology modeling structure of LDC and Ldc1E.

<p>(A) Superposition of the Ldc1E monomer (yellow) on the LDC from <i>E</i>. <i>coli</i> K-12 (PDB ID: 3n75). (B) Ribbon representation of Ldc1E homo-decamer. (C) Ball-and-stick representation of the docking models of Ldc1E with PLP. Lys367 was a catalytic residue located in the active center, and the Trp333, Ser364, and His366 stabilized the PLP structure. (D) Ball-and-stick representation of the docking models of Ldc1E with L-lysine, where Lys367, Val524, and Glu526 were probably substrate binding sites.</p

Phylogenetic tree analysis of the Ldc1E protein with other known LDCs based on the amino acid sequences.

<p>A phylogenetic tree was constructed using the neighbor-joining method with MEGA 6.0, and 1,000 bootstrap replicates were indicated at branching points. Ldc1E was shown with a solid triangle. The tree also shows the GenBank accession number and original genus of other LDCs, with the scale bar representing the number of changes per amino acid position.</p