A Comprehensive Network Integrating Signature Microbes and Crucial Soil Properties During Early Biological Soil Crust Formation on Tropical Reef Islands

Abstract

Biological soil crusts (BSCs/biocrusts), which are distributed across various climatic zones and well-studied in terrestrial drylands, harbor polyextremotolerant microbial topsoil communities and provide ecological service for local and global ecosystem. Here, we evaluated BSCs in the tropical reef islands of the South China Sea. Specifically, we collected 41 BSCs, subsurface, and bare soil samples from the Xisha and Nansha Archipelagos. High-throughput amplicon sequencing was performed to analyze the bacterial, fungal, and archaeal compositions of these samples. Physicochemical measurement and enzyme activity assays were conducted to characterize the soil properties. Advanced computational analysis revealed 47 biocrust-specific microbes and 10 biocrust-specific soil properties, as well as their correlations in BSC microbial community. We highlighted the previously underestimated impact of manganese on fungal community regulation and BSC formation. We provide comprehensive insight into BSC formation networks on tropical reef islands and established a foundation for BSC-directed environmental restoration.

Keywords: biocrust formation; biological soil crust; enzyme activity; geographical distribution pattern; microbiome; tropical reef island.

FIGURE 1

Dissimilarity of bacterial, fungal, and archaeal compositions in biocrusts comparing to sub-surface and bare soil samples. Ordination using NMDS is derived from Bray–Curtis dissimilarity and applied to analyze the archaeal (A), fungal (B), and bacterial (C) communities. Circle shape represents soils from Nansha Archipelagos whereas triangle represents Xisha Archipelagos. Different soil types are color coded. The function envfit from the R vegan package was used to fit environmental vectors onto the ordination (environmental factor significant correlation with NMDS, P < 0.05). NMDS, non-metric multidimensional scaling; NS, Nansha Archipelagos; XS, Xisha Archipelagos; BS, bare soil; BSC_sub, biocrust subsurface soil; BSCs, biocrusts; Mn, soil available manganese; NO₃-N, soil nitrate nitrogen; NH₃-N, soil ammonia nitrogen; B, soil available boron; S, soil available sulfur.

FIGURE 2

Archaeal, fungal, and bacterial OTUs with significantly altered abundance in BSCs comparing to BS and BSC_sub. Volcano plots represent the significantly increased (green) and decreased (red) OTUs (DESeq2, Benjamini-Hochberg adjusted p-value < 0.01, fold-change within top and bottom 5%) in archaeal (A), fungal (B), and bacterial (C) communities in BSCs comparing to BS and BSC_sub as indicated. Log2-transformed fold-change values of the relative abundance (X-axis) are plotted against adjusted P-values (unify P-value across the main text) (Y-axis). Venn diagrams illustrate the statistics of significantly increased and decreased OTUs corresponding to the right or bottom panel. Families with the top2 highest numbers of significantly co-altered OTUs are denoted as Phylum_Family (co-altered OTU number). BS, bare soil; BSC_sub, biocrust subsurface soil; BSCs, biocrusts.

FIGURE 3

Analysis of habitat specialists and generalists. Niche breadth of OTUs identified across all sample types (BS, BSC_sub, and BSCs). Each symbol represents an OTU. OTUs that are present along a wider range of habitats have a higher niche breadth value and are considered habitat generalists (green), while OTUs with a niche breadth value < 1.5 are considered habitat specialists (red), and the black circles represent OTUs that could not be defined as generalists or specialists. Generalists with highest abundance (ubiquity cutoff: 94%, abundance cutoff: 4%) are considered as core generalists (green triangle). Specialists with significant INDVAL values (cutoff: >0.3) are specialists for BSCs (red triangle). Numbers outside of the square was represent the number of OTUs for each category. BS, bare soil; BSC_sub, biocrust subsurface soil; BSCs, biocrusts.

FIGURE 4

Weighted gene co-expression network analysis (WGCNA). The correlation among 53 modules (Y-axis) and 31 soil properties (X-axis) are illustrated in the heatmap. Positive correlation value is represented by red and negative by blue. The “*” in the cells are presented as microbial module significantly correlating with soil properties (P < 0.05). Pie charts on the right side of the indicated modules represent the percentage of significantly increased (red) and decreased (blue) OTUs in biocrust. Pp, Precipitation; B, Soil Available Boron; OM, Organic Matter; OC, Organic Carbon; SAP, Soil Available Phosphorus; SEC, Soil Exchangeable Calcium; SAK, Soil Available Kalium; K, Kalium; Ca, Calcium; Zn, Soil Available Zinc; Cu, Soil Available Copper; Fe, Soil Available Iron; Mn, Soil Available Manganese; TWSS, Total Water Soluble Salt; STP, Soil Total Phosphorus; S, Soil Available Sulfur; STN, Soil Total Nitrogen; NO₂-N, Soil Nitrite Nitrogen; NO₃-N, Soil Nitrate Nitrogen; NH₄-N, Soil Ammonium Nitrogen; NH₃-N, Soil Ammonia Nitrogen; Chl a, chlorophyll a; S-β-GC, soil β-glucosidase activity; S-LPS, soil lipase activity; S-FDA, soil FDA hydrolase activity; S-ALPT, soil alkaline protease activity; S-UE, soil urease activity; S-AKP, soil alkaline phosphatase activity; S-CAT, soil catalase activity.

FIGURE 5

The network analysis revealing the correlation of the key properties with the signature OTUs. A correlation between two items was considered statistically robust if the absolute value of Spearman’s correlation coefficient (ρ) was > 0.35 and the P < 0.05. The nodes were the signature OTUs and the key properties, which from microbial modules, module 28 (A), module 20 (B), module 30 (C), module 23 (D), and module 31 (E). OTUs were colored according to OTUs classification information. The size of each node was proportional to the number of connections. Graphics were generated in Cytoscape 3.5.1 using a circular layout. Chl a, chlorophyll a; GC, soil β-glucosidase activity; FDA, soil FDA hydrolase activity; UE, soil urease activity; CAT, soil catalase activity; NO₃-N, soil nitrate nitrogen.