Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem

Abstract

Background Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. Results The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. Conclusions This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats.

Linking prokaryotic genome size variation to metabolic potential and environment

“…Complementarily, previous results show that the Dead Zone bacteria tend to be more metabolically similar to each other when compared to bacteria from oxic sediments (Broman et al, 2022). Our observation confirms a recent study that observed microaerophilic microorganisms from diverse environments present smaller genome sizes than obligate anaerobic (Nielsen et al, 2021).…”

“…The top 2 cm of sediment was collected at soft bottom clay-muddy habitats from 59 stations from north to south in the Baltic Sea in 2019, following the sampling described in Broman et al, (2022) ( Supplementary Table 1 for coordinates). Briefly, one sediment core was collected per station using a Kajak gravity corer (surface area: 50 cm 2 , one core per station) and the top 0–2 cm layer was sliced into a 215 ml polypropylene container (207.0215PP, Noax Lab, Sweden).…”

“…The final dataset consisted of 219 metagenome samples from a wide range of locations in the Baltic Sea that include 5 independent datasets (Supplementary Table 1 and Figure 1). We compiled 108 sediment metagenomes, of which 59 were collected in 2019 and recently published (Broman et al, 2022), and we collected 49 metagenomes from 2016 to 2018. The pelagic dataset consists of 118 pelagic samples collected from 2011 to 2015 published in three different studies (Alneberg et al, 2020(Alneberg et al, , 2018Larsson et al, 2014).…”

“…Environmental sampling. The top 2 cm of sediment was collected at soft bottom clay-muddy habitats from 59 stations from north to south in the Baltic Sea in 2019, following the sampling described in Broman et al, (2022) (Supplementary Table 1 for coordinates).…”

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients

“…A few studies reported maricultural farms as a point-source ( Lin et al, 2015 ; Muziasari et al, 2016 ; Gao et al, 2018 ) and terrestrial runoffs as a primary non-point source ( Chen et al, 2013a , b ) leading to the enrichment of ARGs in coastal sediments. Terrestrial runoffs commonly lead to multiple environmental gradients from bay to offshore areas ( Hou et al, 2014 ; Wang et al, 2015 ; Zhang H. et al, 2018 ; Broman et al, 2022 ). However, our knowledge about geographic patterns of antibiotic resistomes in sediments across coastal ecological gradients is still lacking.…”