Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?

Abstract

The effect of nutrients on microbial interactions, including competition and collaboration, has mainly been studied in laboratories, but their potential application to complex ecosystems is unknown. Here, we examined the effect of changes in organic acids among other parameters on snow microbial communities in situ over 2 months. We compared snow bacterial communities from a low organic acid content period to that from a higher organic acid period. We hypothesized that an increase in organic acids would shift the dominant microbial interaction from collaboration to competition. To evaluate microbial interactions, we built taxonomic co-variance networks from OTUs obtained from 16S rRNA gene sequencing. In addition, we tracked marker genes of microbial cooperation (plasmid backbone genes) and competition (antibiotic resistance genes) across both sampling periods in metagenomes and metatranscriptomes. Our results showed a decrease in the average connectivity of the network during late spring compared to the early spring that we interpreted as a decrease of cooperation. This observation was strengthened by the significantly more abundant plasmid backbone genes in the metagenomes from the early spring. The modularity of the network from the late spring was also found to be higher than the one from the early spring, which is another possible indicator of increased competition. Antibiotic resistance genes were significantly more abundant in the late spring metagenomes. In addition, antibiotic resistance genes were also positively correlated to the organic acid concentration of the snow across both seasons. Snow organic acid content might be responsible for this change in bacterial interactions in the Arctic snow community.

Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds

“…We also found that in the late spring samples the abundance of sequencing reads mapping to the components of the fatty acid synthesis-related microbial pathways significantly correlated with organic acid levels. Both of these findings are consistent with a period of microbial community growth, in line with the previous finding of the switch from microbial cooperation to competition [33]. We further observed that the rise in organic acid levels correlated with the appearance of the geraniol degradation pathway and disappearance of the styrene degradation pathway.…”

“…With the warming in the late spring, the active community made up a larger fraction of the sequenced reads and, thus, manifested in more homogeneity. Previous 16S rRNA-based taxonomic analysis on the same dataset observed a shift in the community from early to late spring [33]. While the early spring samples contained a core community of 59 OTUs, there were only 29 OTUs in the late spring samples, with 42 early spring core OTUs disappearing from the core community of late spring samples [33].…”

“…We obtained the metagenomic, metatranscriptomic, and chemistry data for twenty snow samples from the ftp website from the Environmental Microbial Genomic Group (ftp://ftp-adn.eclyon.fr/Snow_organic_acids_bacterial_interactions/metagenomes_and_metatranscriptomes_svalbard2011 /). The technical details of the sampling and sequencing process were described in a previous study [33]. Briefly, snow was collected over two months during mid-April to mid-June at Ny Ålesund in the Spitsbergen Island of Svalbard, Norway (78°56'N, 11°52'E).…”

“…Surface snow layers were collected into sterile bags using a sterilized shovel from a 50 m2 perimeter with restricted access to reduce contamination from human sources. Details on sampling conditions, sample site and chemical analyses can be found in Bergk-Pinto et al [33].…”

“…Bergk-Pinto et al studied the microbial ecology in twenty snow samples collected during early and late spring (mid-April to mid-June, 2011, Svalbard, Norway) [33]. Using a combined method of marker genes and network analysis, Bergk-Pinto et al revealed that from early to late spring, the microbial community in the snow shifted from cooperation to competition, accompanied by enrichment of antibiotic resistant genes [33]. Here, we investigated microbial metabolism of organic compounds at low temperature and further analyzed these metagenomic and metatranscriptomic datasets using mi-faser [27].…”