Identification of subannual patterns in microbial community signatures from individual sedimentary laminae using a freeze-coring approach

Abstract

Discrete biological community signatures were identified in individual sub-annually deposited sedimentary laminae of anoxic lake sediments from two lakes in the Minneapolis-St. Paul (Minnesota, U.S.A.) urban area. Recognizing variation in microbial communities associated with discrete millimeter scale sedimentary horizons was made possible using a freeze-coring method to recover bacterial DNA for amplicon iTag sequencing and Terminal Restriction Fragment Length Polymorphism analyses. Variation in 16S rRNA gene composition between laminae suggests that seasonal changes in cell transport from the water column impart a residual molecular signature on subsurface communities. Direct comparison of frozen-in-situ core samples to ambient temperature sediment indicates that freeze coring methodology imposes no significant bias on DNA-based community fingerprints. This work further supports previous observations demonstrating the efficacy of freeze coring for high-resolution analysis of microbial communities, but here it is applied to resolving molecular signatures derived from sedimentary laminae.

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite‐associated sediment profiles

“…Peak relative abundance of 16S rRNA gene sequences clustering within the Cyanobacteria (7.6%) was observed at 48.5 cmbi in the Twin Lake sediment core directly overlying the studied turbidite deposit. We interpret the <1‐cm‐thick peak as an exceptional phytoplankton bloom event due to preservation of phototroph DNA relative to other sampled depths in the present study and previous investigation of Twin Lake surface sediment (Harrison et al., ). Although fermentation has been observed in some Cyanobacteria under dark, anoxic conditions (Stal and Moezelaar, ), the Twin Lake sediment sequences primarily cluster with Prochlorococcus lineages not known to subsist under these conditions.…”

“…Previous studies have noted that Betaproteobacteria are common components of freshwater lake surface sediments under oxic and suboxic conditions (Briée, Moreira, & López‐García, ; Haller et al., ; Spring, Schulze, Overmann, & Schleifer, ; Zwart, Crump, Kamst‐van Agterveld, Hagen, & Han, ). Burkholderiales sequences were detected at ~3% relative abundance in the uppermost 10 cm of Twin Lake and nearby oligomictic Lake McCarrons (Harrison et al., ). Elevated abundance within the turbidite could therefore be explained by entrainment of material from shallower sediments in which oxygen and nitrate‐replete metabolisms would be more favorable.…”

“…A ~1‐m sediment freeze core was collected at 15.5 m water depth from meromictic Twin Lake (TL; Golden Valley, Minnesota; 44°59′N, 93°20′W; 0.09 km 2 ) in February, 2013, as previously described (Harrison et al., ). Oxygen depletion was observed at ~11 m water depth using a YSI‐85 Multimeter (YSI Inc., Yellow Springs, OH, USA).…”

“…Previous work has demonstrated that DNA extracted from unconsolidated sediments may retain records of microbial communities from the time of sediment deposition. Transient changes to planktonic microbial communities impart relict DNA signatures of phototrophic bacteria in lake and marine sediments (e.g., Coolen & Overmann, , ; Harrison, Myrbo, Flood, & Bailey, ). The resiliency of extracellular DNA and dormant cells to overprinting and degradation has led some authors to identify a microbial “paleome” of ancient DNA in deep subsurface sedimentary environments (Inagaki, Okada, Tsapin, & Nealson, ; Orsi, Biddle, & Edgcomb, ).…”

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

“…Interestingly, both coastal sites revealed relatively high abundances of Bathyarchaeota and Thaumarchaeota Group C3 (G-C3), while at site US5B these groups were in the minority. Available genomes of Bathyarchaeota suggest their involvement in methylotrophic methanogenesis, anaerobic methanotrophy (Evans et al 2015;Harris et al 2018), detrital protein degradation, and/or fermentative acetate production (Lloyd et al 2013;He et al 2016;Lazar et al 2016). The metabolism of Thaumarchaeota G-C3 remains somewhat enigmatic since no enrichments or genomic sequences are available yet.…”