Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.

Scott C Thomas,Paul Dijkstra,Cale O Seymour,Jeremy A Dodsworth,Kevin O Tamadonfar,Emiley A Eloe-Fadrosh,Senthil K Murugapiran,Brian P Hedlund,Dengxun Lai

doi:10.3389/fmicb.2019.01427

Abstract

Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ 13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.

Highlights

Temperature is a primary driver of taxonomic diversity of microbial communities (Cole et al, 2013; Sharp et al, 2014; Sunagawa et al, 2015; Power et al, 2018), with an observed maximum at 25◦C and decreasing diversity as temperature becomes more extreme (Sharp et al, 2014)
Analysis of filtered 16S rRNA gene amplicons showed that observed richness ranged from 113 to 491 species-level operational taxonomic units (OTUs) (3%), while Chao1 estimated richness values ranged from 291.75 to 833.16 (Table 2)
All diversity metrics decreased as temperature increased, the Great Boiling Spring (GBS) 85 site consistently demonstrated the lowest values (Table 2; Table S2)

Summary

Introduction

Temperature is a primary driver of taxonomic diversity of microbial communities (Cole et al, 2013; Sharp et al, 2014; Sunagawa et al, 2015; Power et al, 2018), with an observed maximum at 25◦C and decreasing diversity as temperature becomes more extreme (Sharp et al, 2014). This temperaturedriven diversity gradient provides an opportunity to assess the consequences of decreasing taxonomic diversity on ecosystem function (Swingley et al, 2012). The upper-temperature limit for photosynthesis is ∼73◦C (Brock, 1967; Cox et al, 2011; Boyd et al, 2012) and the uppertemperature limit for chemolithotrophic nitrite oxidation may be ∼65◦C (Lebedeva et al, 2005; Sorokin et al, 2012; Edwards et al, 2013), suggesting temperature can be a strong driver of not just taxonomic diversity and functional diversity

Methods

Results

Conclusion