Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

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From: PLoS ONE(Vol. 7, Issue 6)
Publisher: Public Library of Science
Document Type: Article
Length: 12,691 words
Lexile Measure: 1650L

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Author(s): Wesley D. Swingley 1 , D'Arcy R. Meyer-Dombard 2 , Everett L. Shock 3 , 4 , Eric B. Alsop 3 , Heinz D. Falenski 3 , Jeff R. Havig 3 , Jason Raymond 3 , *

Introduction

The continuous microbial community along the outflow of "Bison Pool" (BP), Yellowstone National Park (YNP), is an ideal system for understanding how the ecological stress of a temperature gradient, and the corresponding change in pH and geochemistry, drives microbial community development. BP, a slightly alkaline (pH 7.3-8.3) spring in the Sentinel Meadows basin, has been the target of recent interest linking geochemistry to microbial community structure, the formation of streamer biofilm communities in the chemosynthetic zones (>68°C), isotopic composition of biofilms, and protein inventories [1], [2], [3], [4]. This steady-flow, boiling spring features a silica-encrusted source pool with a single run-off channel that supports a gradient of microbial communities as the boiling source-water cools 40°C in just over 20 m. The physicochemical features of BP provide a test bed for hypotheses related to changes in microbial communities, metabolic capacity, and biogeochemical cycling as a function of downstream flow. Our guiding hypotheses were: 1) observations of shifts in microbial communities should mirror shifts in the dominance of metabolic "lifestyles", with distance down the outflow channel. 2) community and genetic capacity for facilitating biogeochemical cycling should shift as a function of environmental conditions at different points in the outflow, and 3) while unique environments exist in the outflow channel, we will find evidence for both specialists and generalists in this thermophilic ecosystem. These relationships are explored here, using a metagenomic dataset collected at consecutive points down the BP outflow channel.

Metagenomic data have been reported from single communities, featuring as few as one dominant species [5], [6], [7], and from multiple geographically-distinct communities [8], [9], [10], [11], [12]. In communities with relatively few dominant species, the separation and assembly of species-specific sequences yielded complete or nearly complete genome assemblies [5], [6], [7]. Conversely, the complex, oligotrophic environments sampled during the Sorcerer II Global Ocean Sampling Expedition yielded few large assemblies, despite the addition of a long paired-end fosmid library designed to facilitate assembly [11], [12]. Here we present environmental genome sequence from biofilms at five contiguous sites along the source and outflow channel of BP-hereafter referred to as the "Bison Pool" Environmental Genome (BPEG). This is the first report of metagenome data of multiple, geochemically- and physically-related samples from a hydrothermal system.

Only within the past decade has whole-community DNA sequencing become feasible [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], often necessitating the development of novel analysis packages in order to analyze these enormous datasets [15], [16], [17], [18], [19], [20], [21], [22], [23]. One of the key steps in dissecting the morass of data within a metagenome is the assignment of individual sequencing reads/scaffolds/contigs to taxonomic bins [24], [25]. This process, called "binning," not only reduces the volume of information, but allows the reconstruction of metabolic models for single...

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Gale Document Number: GALE|A477116652