Depth shapes α‐ and β‐diversities of microbial eukaryotes in surficial sediments of coastal ecosystems

Abstract

SummaryLittle is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and operational taxonomic unit (OTU) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth-decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped β-diversity of benthic microeukaryotes (including both the abundant and the rare biosphere) on a regional scale. Similar hydrographic and mineralogical factors contributed to the biogeography of both the abundant and the rare OTUs. The trace metal vanadium had a significant effect on the biogeography of the rare biosphere. Our study sheds new light on the composition, diversity patterns and underlying mechanisms of single-celled eukaryote distribution in surficial sediments of coastal oceans.

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

“…Because finer fractions carry most of the metals in natural sediments (48), we expected that markedly higher concentrations of many metals would be found in the vegetated than in the bare sediments. Compared with the metal concentrations in surface sediment samples collected from deeper sites (15 to 75 m) in the Bohai Sea and the Yellow Sea, where the sediment grain size was much finer (49), the concentrations of all metals, with the exception of Cd, were markedly lower in the present study, suggesting worse Cd pollution in Swan Lake.…”

Responses of denitrifying bacterial communities to short-term waterlogging of soils

“…Therefore, a combination of nutrient selection and poor dispersal may have resulted in differences in microbial-community compositions. Because the level of both water-soluble carbon and nitrate-N showed clear gradients based on soil depth (see Supplementary Table S8), soil depth might be a proxy for various nutrients in soil as suggested in coastal ecosystems 55 . For each gene, our identification of different enriched OTUs at each soil depth (see Supplementary Table S11) might be explained as the result of selection and limited dispersal.…”

Abundant and Rare Bacterioplankton in Freshwater Lakes Subjected to Different Levels of Tourism Disturbances

“…Subsequently, separate tables of abundant and rare OTUs were generated. To normalize sequences for comparison, we rarefied all datasets to the lowest number of sequences for community-diversity analysis [30,48]. In our study, 24,985 and 711 sequences were the lowest number of sequences recovered for abundant and rare taxa, respectively (Table S1).…”

“…Consistent with recent studies [30,48,49], we followed the arbitrary definitions of abundant and rare OTUs in relation to their local relative abundance for downstream analysis. To facilitate the comparisons, we adopted thresholds following References [31,50].…”

“…The rarefaction curves of the bacterial community were observed to be approximately planar ( Figure S3), suggesting that sequencing was sufficient in this study for the samples from all lakes. To minimize the bias connected with sequencing coverage [31,48], we randomly selected 26,852 sequences (the lowest number of sequences for the whole dataset) from each sample for data analysis. At a 3% dissimilarity level, a total of 2487 OTUs were detected from 322,224 (=12 × 26,852) sequences.…”