Aquifer environment selects for microbial species cohorts in sediment and groundwater

Abstract

Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

“…Using an approach outlined in ref. 38, subassemblies were performed to reconstruct the dominant genomes in the day 13 and day 82 samples, using 10 and 8% of the reads, respectively. Results from the subassemblies are included (Supplementary Table 2).…”

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

“…Through geophysical measurements, Wainwright et al (2015) has estimated that ∼3% of the aquifer volume is composed of NRZ-type sediments. Coupled to these mineralogical and geochemical observations, community genomic tools have been used to identify key microbial groups likely catalyzing many of the redox reactions that contribute to overall ecosystem functions within the aquifer (Wrighton et al, 2012(Wrighton et al, , 2014Castelle et al, 2013Castelle et al, , 2015Kantor et al, 2013;Hug et al, 2015). However, most of these studies have occurred over limited temporal scales, and have focused on highly reduced regions of the aquifer.…”

Organic contamination versus mineral properties: competing selective forces shaping bacterial community assembly in aquifer sediments

“…Another point of interest refers to ecological theory with respect to microbial community assembly at a local and regional scale (Lindström & Langenheder 2012). A highly contaminated zone within an aquifer characterized by highly specific microbial communities, as introduced in the present study, constitutes a continuous source of species and specific functions to downgradient environmental compartments including surface waters and soils (Hug et al 2015). …”

“…top-down control on bacterial communities via protozoan grazing and viral lysis (Šimek et al 2003, Kent et al 2007, Salcher et al 2005, Wey et al 2008, await evaluation. Also, the temporal dynamics of sediment bacterial communities caused by the continuous exchange of cells between the water and sediment phase need to be tested (Zhou et al 2012, Hug et al 2015. Another point of interest refers to ecological theory with respect to microbial community assembly at a local and regional scale (Lindström & Langenheder 2012).…”

“…Early research demonstrated that attached populations may exhibit distinct cell morphology ) and physiology (Köl-bel-Boelke & Hirsch 1989, Hirsch 1992, Watnick & Kolter 2000. More recently, it has been confirmed that suspended and attached prokaryotic communities most often show striking differences also in community composition (Reardon et al 2004, Flynn et al 2008, Griebler & Lueders 2009, Anneser et al 2010, Rizoulis et al 2013, Hug et al 2015. The factors responsible include those mentioned above as well as additional ones such as the chemical composition of the groundwater, substrate, and electron acceptor availability, the redox conditions and, explicitly, the impact of contaminants (Griebler & Lueders 2009, Rizoulis et al 2013).…”