Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments

Abstract

Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. The high-resolution mechanisms of the vertical assembly processes in marine sediments remain poorly described. We analyzed 31 depth layers of 3 sediment cores from the shallow sediment zone at 3 stations in the Bohai Sea, and obtained high-resolution vertical profiles (2 cm per sample) of microbial communities. We analyzed 78 archaeal and 76 bacterial communities based on 16S rRNA gene amplicon sequencing, together with 14 selected metagenomes. We grouped these samples into three layers (Top, 0-18 cm; Middle, 18-38 cm; and Bottom, below 38 cm) to analyze trends in diversity and assembly processes along the depth gradient. We found that alpha diversity increased for the Thaumarchaeota-dominated archaeal community but decreased for the Proteobacteria-dominated bacterial community as depth increased. The mechanisms determining archaeal community assembly were mostly deterministic, while bacterial community assembly was mostly stochastic. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundance ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.

Globally distributed marine Gemmatimonadota have unique genomic potentials

“…Some Group2 MAGs (16/85) also appear to be capable of reducing sulfate. These DsrAB sequences were mostly associated with MAGs recovered from deep sediments (below 30 cm) in BS, where high concentrations of sulfate were detected (> 22 mmol/L in pore water) 15 . DsrAB genes (Supplementary Figs.…”

“…Total DNA was extracted from each sample and sequenced after quality control as described in the corresponding references 15,34,104,105 . The sequences were assembled and binned with different protocols based on the batch of the samples 34,105 .…”

“…BS samples were collected from sediments at three stations BHB10, M3, and M8 in the BS, China. Details of sampling sites and procedures were described previously 15 . SFB samples were collected from sediments in the San Francisco Bay, U.S. across four seasons (July, October, January, and May) between July 2011 and May 2012 104 .…”

“…Their abundance increased during drought conditions 14 , suggesting an active response to the change in soil moisture. In coastal sediments, Gemmatimonadota showed strong correlations with different key genes involved in sulfur, nitrogen, and oxygen metabolism 15 . At present, Gemmatimonadota contains six cultured species which are chemoorganoheterotrophs, two of which have the purple bacterial reaction centers for anoxygenic photosynthesis 16,17 .…”

New globally distributed bacterial phyla within the FCB superphylum

“…Sampling details for hydrothermal samples from GB were described previously 33 . Samples from the BS were collected using a stainless steel box-sampler 50 . An 11 cm diameter polyvinyl chloride (PVC) tube with dark-tape sealed 2 cm interval side-holes was inserted into the box-sampler after carefully removing top water to take sediment core samples.…”