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. 2021 Jun 12;9(6):1291.
doi: 10.3390/microorganisms9061291.

Structural and Functional Impacts of Microbiota on Pyropia yezoensis and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea

Arsalan Ahmed  1 , Anam Khurshid  1 , Xianghai Tang  1 , Junhao Wang  1 , Tehsin Ullah Khan  1 , Yunxiang Mao  1   2
Affiliations

Structural and Functional Impacts of Microbiota on Pyropia yezoensis and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea

Arsalan Ahmed et al. Microorganisms. .

Abstract

Pyropia yezoensis is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples (n = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Bacterial communities in association with P. yezoensis and surrounding seawater were predominated by Cyanobacteria, Proteobacteria, and Bacteroidetes. The variability of bacterial communities related to P. yezoensis and seawater were predominantly shaped by nitrate (NO3), ammonium (NH4), and temperature. Cluster analysis revealed a close relationship between thalli (RTH and YTH) and seawater (RSW and YSW) in terms of the residing bacterial communities, respectively. PICRUSt analysis revealed the presence of genes associated with amino acid transportation and metabolism, which explained the bacterial dependence on algal-provided nutrients. This study reveals that the diversity of microbiota for P. yezoensis is greatly influenced by abiotic factors and algal organic exudates which trigger chemical signaling and transportation responses from the bacterial community, which in turn activates genes to metabolize subsequent substrates.

Keywords: Illumina NovaSeq; Pyropia yezoensis; bacterial communities; microbial composition; microbiome; ribosomal RNA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(A) P. yezoensis thalli. (B) Yantai cultivation farm. (C) Rizhao cultivation farm.
Figure 2
Figure 2
Comparisons of alpha diversity indices based on an unpaired Wilcoxon rank-sum test: (A) observed species; (B) Shannon; (C) Simpson; (D) Chao1; (E) ACE; (F) PD whole-tree. YTH, Yantai region thalli of P. yezoensis; YSW, Yantai region seawater sample group; RTH, Rizhao region thalli of P. yezoensis; RSW, Rizhao region seawater sample group. (* p-value < 0.05; ** p-value < 0.01).
Figure 3
Figure 3
Relationships between individual datasets illustrated by (A) principal component analysis (PCA) and (B) nonmetric multi-dimensional scaling (NMDS).
Figure 4
Figure 4
(A) UPGMA cluster tree analysis based on the unweighted UniFrac distance. The digital number symbolizes three biological replicates for each sample. (B) Evolutionary branch diagram of differential bacterial communities or species. (C) The LDA value (influence value of linear discriminant analysis) distribution histogram shows bacterial communities or species (Biomarker) with a LDA score greater than four.
Figure 5
Figure 5
Bacterial community structures associated with P. yezoensis and seawater at the phylum and class levels. YTH, Yantai region P. yezoensis thalli; YSW, Yantai region seawater; RTH, Rizhao region P. yezoensis thalli; RSW, Rizhao region seawater.
Figure 6
Figure 6
(A) Heat map display of the hierarchical clustering of the predicted KEGG ortholog (KEGG level 3) gene copy number (log10 transformed) of bacterial microbiota across all samples. (B) Cluster heat map display of KOs based on the predicted gene copy (log10 transformed) of bacterial microbiota across all sample groups. K00059 fabG, K01692 paaF, K02049 ABC.SN.A,K02035 ABC.PE.S, K03183 ubiE, K01362 OVCH, K02040 pstS, K01491 folD, K06147 ABCB-BAC, K03496 parA, K03798 ftsH, K00384 trxB, K03087 rpoS, K02639 petF, K05575 ndhD, K07496 putative transposase, K08884 serine/threonine protein kinase, K00799 GST, K02434 gatB, K02433 gatA, K02014 TC.FEV.OM, K03088 rpoE, K00540 fqr, K01834 PGAM, K09687 Antibiotic transport system, K02004 ABC.CD.P, K02003 ABC.CD.A, K01990 ABC-2.A, K00936 pdtaS, K03797 ctpA, K03711 fur, K02005 ABC.CD.TX, K03671 trxA, K01992 ABC-2.P, K13789 GGPS.
Figure 7
Figure 7
(A) Redundancy analysis (RDA) for bacterial community datasets associated with P. yezoensis and seawater. T, temperature; P, phosphate; RS, reactive silicate. (B) Spearman correlation analysis between seawater environmental factors and bacterial communities. The corresponding intermediate heat map value is the Spearman correlation coefficient r, and r > 0 is the positive correlation, r < 0 is negative correlation. * indicates significance where p < 0.05. ** indicates significance where p < 0.01.
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