The preservation of microbial DNA in archived soils of various genetic types

Abstract

This study is a comparative analysis of samples of archived (stored for over 70–90 years) and modern soils of two different genetic types–chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.

Protecting the unseen majority: Land cover and environmental factors linked with soil bacterial communities and functions in New Zealand

“…Although the technology is still developing, the analysis of archived soil samples using ancient DNA techniques (e.g. Martin-Laurent et al 2001;Ivanova et al 2017), may eventually be able to help reconstruct New Zealand's soil ecosystems over extended time periods and address these critical biodiversity and conservation questions. Perhaps New Zealand can create another catalogue of lost species?…”

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?

“…Further, we sought to identify those taxa that were the most resilient and sensitive soil archival. Our results demonstrate that soil samples preserved by air-drying and long-time soil archival can be used to identify differences in microbial communities along different temporal, spatial and organizational scales, as well as in response to soil traits and management [ 9 , 12 , 52 ]. However, we did find that fungal and prokaryotic diversity both decrease with time, and that this response differed between taxa and study sites.…”

“…For example, the ratio of soil enzymatic activity was found to be more significantly affected by freezing than by drying, especially in soil with high C (carbon) content, when compared to fresh soil [ 10 , 11 ]. A reduction in prokaryotic diversity was recently found in soil archives of the Central Museum of Soil Science in Russia, which had been air-dried and stored for over 70 years, relative to prokaryotic diversity in fresh soils [ 12 ]. Over short-term durations, Lauber et al in 2010 [ 13 ] used high-throughput pyrosequencing of prokaryotic 16S rRNA to show that structure and diversity of prokaryotes in dried, frozen or soils stored at room temperature were not significantly different from fresh soil samples [ 13 ].…”

The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons

“…Air-dried, archived soils have been extensively studied and represent a valuable resource for soil microbiologists due to the cost and space required to maintain frozen soil samples (Cary and Fierer, 2014;Dolfing and Feng, 2015). However, the community composition of archived, air-dried soils is significantly different from frozen/fresh soils and careful consideration is required when analyzing air-dried soil that has been stored for long periods (years) (Dolfing et al, 2004;Clark and Hirsch, 2008;Tzeneva et al, 2009;Ivanova et al, 2017). Streptomyces produce desiccation resistant spores that can survive dry conditions for many years (Ensign, 1978).…”

“…One possible explanation is that non abundance weighted metrics may not achieve the same sensitivity as their abundance weighted counterparts (Stegen et al, 2012(Stegen et al, , 2015. However, abundance weighting of βRC as RCbray (Stegen et al, 2013) is inappropriate for dry-stored soils for which sample abundance might not represent in situ abundance (Clark and Hirsch, 2008;Ivanova et al, 2017). While the βRC metric is also influenced by the size of the regional species pool selected (Chase et al, 2011), Streptomyces spores can be readily dispersed by insects or wind (Lloyd, 1969;Ruddick and Williams, 1972), and the choice of the totality of NZ as a regional Streptomyces species pool is not unrealistic.…”