Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples

Brandt, Franziska B.; Breidenbach, Björn; Brenzinger, Kristof; Conrad, Ralf

doi:10.1016/j.syapm.2014.10.007

Cited by 17 publications

(19 citation statements)

References 45 publications

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“…Results for HXD consumption within the samples collected at a depth of 15 m (A and B) showed a similar degradation rate ( A = 5.94 mg HXD/L per day and B = 5.52 mg HXD/L per day), with 89.38% removal efficiency, compared to samples taken from 200 m depth (C and D) where the consumption rate was much slower ( C = 1.58 mg HXD/L per day and D = 0.76 mg HXD/L per day); nevertheless, the same removal efficiency rate was observed (93.44%). It was also observed that the storage temperature (−20 °C) did not affect the activity of HXD consumption in sediments, as reported by Rubin et al and Brandt et al…”

Section: Discussionsupporting

confidence: 76%

“…Two samples from the coastal zone at a depth of 15 m and two from the oceanic zone at a depth of 200 m were taken (Figure ). Samples were kept frozen (−20 °C) until analyzed at CINVESTAV‐IPN, Merida laboratory; this temperature does not induce drastic changes in the composition and abundance of microbial communities as has been reported elsewhere …”

Section: Methodsmentioning

confidence: 99%

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Microbial Activity in Marine Sediments Exposed to Hexadecane: A Laboratory Study

Gamboa-Muñoz

García-Cruz

Ramos-Castillo

et al. 2017

CLEAN Soil Air Water

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Bacteria have developed metabolic pathways that allow them to use hydrocarbons as the source of carbon and energy, so that they now play a key role throughout the degradation of petroleum in natural environments. However, knowledge regarding the degradation of petroleum by microorganisms is far larger in soils than in marine environments. Hexadecane (HXD) is one of the most representative alkanes present in petroleum, and one of the most frequently used in laboratory trials to evaluate the degradation of hydrocarbons by microorganisms. In this study, the capacity for HXD degradation by microorganisms present in marine sediments collected at 15 and 200 m depth is determined experimentally. For 42 days, kinetics studies are carried out to measure the consumption of HXD. Every 7 days the number of colony forming units (CFU) and HXD concentration are determined. Additionally, a biomass sample for pyrosequencing is collected at the beginning of the experiment (t0), the time of maximum bacterial growth (t7 or t21) and at the end of the experiment (t42). A higher HXD consumption rate is observed in sediments from 15 m with respect to sediments from 200 m depth. The major HXD consumption occurs within the first 7 days for the sediments from 15 m and within 21 days for the sediments from 200 m depth; the biomass concentration CFU follows the same profile. The non‐metric multidimensional scaling analysis of the non‐cultivable bacteria indicates differences between bacteria species composition at different depths, which is confirmed by bacterial identification by pyrosequencing.

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Section: Discussionsupporting

confidence: 76%

Section: Methodsmentioning

confidence: 99%

Microbial Activity in Marine Sediments Exposed to Hexadecane: A Laboratory Study

Gamboa-Muñoz

García-Cruz

Ramos-Castillo

et al. 2017

CLEAN Soil Air Water

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“…The archaeal abundance of wet samples was comparable with the reported abundances in similar habitats like pond sediments (Brandt et al 2014), rich fen (Petersen et al 2012), and estuarine sediments (Webster et al 2015). By contrast, those of the dry samples (1.4 × 10 8 to 2.4 × 10 9 copies (g d.w.s.)…”

Section: Increase Of Archaeal Abundance After Water Floodingsupporting

confidence: 79%

Shifts of archaeal community structure in soil along an elevation gradient in a reservoir water level fluctuation zone

Jiang

et al. 2016

J Soils Sediments

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Purpose Although archaea play an important role in nutrients cycling, the archaeal community in a reservoir water-level fluctuation zone (WLFZ) remains unclear. An elucidation of archaeal community responding to the environmental variables is essential to understand the nutrients dynamics in WLFZ. This study focused on the response of the archaeal community structure and abundance to the periodic water flooding along an elevation gradient in the WLFZ of the Three Gorges Reservoir. Materials and methods Along the elevation gradient (152-175 m) of the study area, soil samples in the beginning and late stages of water flooding were collected to investigate the influence of water flooding on the archaeal community in soil, using quantitative PCR and Illumina high-throughput sequencing approaches.Results and discussion An increase of archaeal abundance from 3.8 × 10 8 to 3.8 × 10 9 copies (g d.w.s) −1 on average was observed after water flooding. The archaeal abundance was positively correlated with the contents of ammonium, organic matter, and moisture in soil and with the accumulated flooding time. Higher diversity was observed in dry samples (non-flooded soil samples) rather than wet samples (flooded soil samples). The Thaumarchaeota were predominant in most of the dry samples. Interestingly, high proportions of Candidatus Nitrososphaera were observed in the transition zone, while euryarchaeotal methanogens dominated the wet samples. The proportion of methanogens decreased dramatically in the dry samples at higher elevations, which was associated with the decrease of the moisture content and the probably increase of available oxygen in soil.Conclusions Archaeal abundance, diversity, and community composition shifted along an elevation gradient and were influenced by water flooding. The increased archaea abundance after water flooding and elevation related community composition and diversity indicated that water flooding was a key dynamic environmental variable in the WLFZ.

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“…Two important sample processing choices that may alter experimental results are (a) the type of soil storage method and (b) DNA extract thaw time, the length of time for which extracted DNA is transported and left to thaw. To date, only a handful of studies have examined consequences of soil storage methods on study results (i.e., temperature, absolute ethanol, freeze‐drying, RNAlater, PLFA) on targets such as DNA, RNA, bacteria, fungi, and arbuscular mycorrhizal fungi (Brandt, Breidenbach, Brenzinger, & Conrad, 2014; Cui et al, 2014; Harry, Gambier, & Garnier‐Sillam, 2000; Klammer, Mondini, & Insam, 2005; Lauber, Zhou, Gordon, Knight, & Fierer, 2010; Rissanen, Kurhela, Aho, Oittinen, & Tiirola, 2010; Rubin et al, 2013; Tzeneva et al, 2009; Weißbecker, Buscot, & Wubet, 2017). These studies have broadly found little impact of storage method, but they do not thoroughly explore common storage practices used in the field and focus overwhelmingly on bacteria.…”

Section: Introductionmentioning

confidence: 99%

Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

Delavaux

Bever

Karppinen

et al. 2020

Ecology and Evolution

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With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at −20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.

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Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples

Cited by 17 publications

References 45 publications

Microbial Activity in Marine Sediments Exposed to Hexadecane: A Laboratory Study

Microbial Activity in Marine Sediments Exposed to Hexadecane: A Laboratory Study

Shifts of archaeal community structure in soil along an elevation gradient in a reservoir water level fluctuation zone

Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

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