Ecology

The Abrolhos shelf extends ~ 200 km offshore and is SWA’s most biodiverse region, encompassing a large mid-to-outer shelf hard bottom domain with reefs and rhodolith beds (~ 20,900 km2)5,6. Fine-sediment dissipative beaches and a large estuary with mangroves dominate the coastline, and terrigenous-mixed sediments predominate in the inner shelf27. This large and complex seascape (Fig. 1) comprises a representative experimental setting for understanding the distribution and abundance of reef fishes in different habitats, as well as for exploring the drivers and spatial scaling of beta diversity in reef fish assemblages. The high richness of reef fishes off coral reefs that we found in Abrolhos was unexpected, and sheds new light toward the integration of phenomena that occur at different scales and across distinct habitats and groups of organisms11,20. From a practical standpoint, our results are relevant to improve marine management in complex tropical seascapes with rhodolith beds23 and other large marginal habitats.
The high richness of reef fishes in rhodolith beds, where fish biomass was smaller than on reefs (Supplementary Fig. S1 online; Fig. 4), seems to be primarily related to the much larger area of rhodolith beds, as well as to the broader depth and cross-shelf range of this hard-bottom habitat, contrasting with reefs. Rather than being a regional idiosyncrasy, the relatively larger area and cross-shelf range of non-reef habitat used by reef fishes seems to be recurrent in tropical shelves across all ocean basins8,9,23. However, due to logistical constrains and to the apparent smaller relevance of marginal habitats to fish and other reef-associated organisms, these habitats are still much less sampled than the iconic shallow water reefs20, with the exception of mangroves and seagrass beds3,8,9.
Compositional variability in biological communities is strongly dependent on spatial scale. Accordingly, beta diversity is expected to be high at biogeographic and local scales, while turnover tends to be lower at regional scales28,29. Reef fish assemblages tend to vary sharply at small spatial scales ( More

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The soil bacterial diversity
The soil bacteriome dataset in this study included 558 soil samples collected from Thailand, the Philippines, Malaysia, and Indonesia (Fig. 1).
Figure 1

The number of soil samples from the selected Southeast Asian countries which were included in this study. The number in each circle represented the number of samples from each country. The Southeast Asia map was redrawn from “Southeast Asia” map (Google Maps retrieved 7 May 2020, from https://www.google.com/maps/@8.2763609,98.123781,4z).

Full size image

Mapping to the global gridded soil information system: SoilGrids21, the soil samples of each selected country encompassed different soil classes (Supplementary Figure S2). The soil from Thailand samples were mostly Acrisols, which comprise clay-rich subsoil with low fertility and high aluminium content. The soil from the Philippines samples were mostly Gleysols, iron-rich wetland soil saturated with groundwater or underwater or in tidal areas. The soil from Malaysia samples were mostly Ferralsols. The soils from Indonesia samples were of mixed soil classes; nearly half (45%) of them belonged to Nitisols, well-drained soil with a moderate-to-high clay content and limited phosphorus availability. Ferralsols took up about 20% of the Indonesia soil samples while another 18% were Histosols (moist soils with thick organic layers). The soil pH levels were significantly different among the soil samples of 4 selected countries (ANOVA, P value  More

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