Patterns of Relative Bacterial Richness and Community Composition in Seawater and Marine Sediment Are Robust for Both Operational Taxonomic Units and Amplicon Sequence Variants

Abstract

To understand the relative influences of operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) on patterns of marine microbial diversity and community composition, we examined bacterial diversity and community composition of seawater from 12 sites in the North Atlantic Ocean and Canadian Arctic and sediment from two sites in the North Atlantic. For the seawater analyses, we included samples from three to six zones in the water column of each site. For the sediment analyses, we included over 20 sediment horizons at each of two sites. For all samples, we amplified the V4–V5 hypervariable region of the 16S ribosomal RNA (rRNA) gene. We analyzed each sample in two different ways: (i) by clustering its reads into 97%-similar OTUs and (ii) by assigning sequences to unique ASVs. OTU richness is much higher than ASV richness for every sample, but both OTUs and ASVs exhibit similar vertical patterns of relative diversity in both the water column and the sediment. Bacterial richness is highest just below the photic zone in the water column and at the seafloor in the sediment. For both OTUs and ASVs, richness estimates depend on the number of sequences analyzed. Both methods yield broadly similar community compositions for each sample at the taxonomic levels of phyla to families. While the two methods yield different richness values, broad-scale patterns of relative richness and community composition are similar with both methods.

Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea

“…Microbial communities of the world’s oceans play an important role in the cycles of biogenic elements on the earth and in maintaining biosphere stability. Therefore, due to the development of molecular methods for studying microbial communities, a large number of studies on the diversity of microorganisms in the marine habitats of our planet have appeared, including both 16S rRNA profiling and metagenomic analyses of different marine habitats [ 33 , 34 , 35 , 36 , 37 ]. Among them are many that focus on microbial communities of the Arctic regions and their spatial and seasonal changes.…”

Investigation of the marine bacterial community along the coastline of the Gulf of Thailand

“…The results of this study revealed a high abundance of bacteria in the phyla Proteobacteria, Bacteroidota, and Cyanobacteria at every sampling site, which corresponded to previous investigations of the microbiome in the seawater of the Gulf of Thailand [ [22] , [23] , [24] ]. These three phyla are also dominant in many other marine environments including the Baltic Sea, Japan Sea, and western North Atlantic [ 21 , 31 ]. However, samples from Prachuap Kiri Khan Province (NHH) showed Thermoplasmatota in high abundance rather than Bacteroidota.…”

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

“…This study provides the first, detailed insight into the composition and the spatial and year-round temporal changes of planktonic and epilithic prokaryotic communities of Danube. High-throughput next generation amplicon sequencing was used with OTU-based calculations applying filters to retain clusters with >0.1% relative abundance, enabling a consistent taxonomy comparison [ 39 – 42 ].…”