Ancient Microbiomes in the Environment

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 656

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Guest Editor
Associate Professor, Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA 6102, Australia
Interests: sedimentary ancient DNA; paleomicrobiology; molecular paleoecology; paleobiogeochemical cycling; paleoenvironment; ocean health; Anthropocene
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Special Issue Information

Dear Colleagues,

The analysis of ancient DNA in sediments (i.e., sedimentary ancient DNA; sedaDNA) using molecular biological tools is rapidly increasing in popularity. The approach offers the ability to reconstruct the diversity, community composition, and functioning of Quaternary coastal marine and terrestrial ecosystems spanning all domains of life (bacteria, archaea, eukarya, and viruses) and their responses to paleoenvironmental perturbations. Moreover, the approach can complement and refine paleoenvironmental and palaeoecological interpretations inferred from the parallel analysis of (in)organic and isotopic geochemical parameters and micro- and macrofossils. We expect that the emerging field will soon offer novel opportunities to vastly increase our knowledge in, for example, microbial genome evolution processes, to predict ecosystem responses in the context of human-induced global changes and to assist geologists in the reconstruction of microbial biogeochemical cycling processes that occurred in deep time.

This Special Issue invites reviews and original contributions to the field of sedaDNA not limited to current accomplishments, future challenges and prospects, and novel methodological approaches (i.e., bioinformatical, biostatistical and analytical tools).

Dr. Marco Coolen
Guest Editor

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Keywords

  • ancient sedimentary DNA
  • molecular paleoecology
  • paleomicrobiology
  • paleoenvironmental perturbations
  • bioinformatics and biostatistics

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Published Papers (1 paper)

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Research

29 pages, 3813 KiB  
Article
A Quaternary Sedimentary Ancient DNA (sedaDNA) Record of Fungal–Terrestrial Ecosystem Dynamics in a Tropical Biodiversity Hotspot (Lake Towuti, Sulawesi, Indonesia)
by Md Akhtar-E Ekram, Cornelia Wuchter, Satria Bijaksana, Kliti Grice, James Russell, Janelle Stevenson, Hendrik Vogel and Marco J. L. Coolen
Microorganisms 2025, 13(5), 1005; https://doi.org/10.3390/microorganisms13051005 - 27 Apr 2025
Viewed by 169
Abstract
Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi–soil–plant interactions, [...] Read more.
Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi–soil–plant interactions, particularly in undersampled, floristically diverse tropical forests. We recently conducted trnL-P6 amplicon sequencing to generate a sedimentary ancient DNA (sedaDNA) record of the regional catchment vegetation of the tropical waterbody Lake Towuti (Sulawesi, Indonesia), spanning over one million years (Myr) of the lake’s developmental history. In this study, we performed 18SV9 amplicon sequencing to create a parallel paleofungal record to (a) infer the composition, origins, and functional guilds of paleofungal community members and (b) determine the extent to which downcore changes in fungal community composition reflect the late Pleistocene evolution of the Lake Towuti catchment. We identified at least 52 members of Ascomycota (predominantly Dothiodeomycetes, Eurotiomycetes, and Leotiomycetes) and 12 members of Basidiomycota (primarily Agaricales and Polyporales). Spearman correlation analysis of the relative changes in fungal community composition, geochemical parameters, and paleovegetation assemblages revealed that the overwhelming majority consisted of soil organic matter and wood-decaying saprobes, except for a necrotrophic phytopathogenic association between Mycosphaerellaceae (Cadophora) and wetland herbs (Alocasia) in more-than-1-Myr-old silts and peats deposited in a pre-lake landscape, dominated by small rivers, wetlands, and peat swamps. During the lacustrine stage, vegetation that used to grow on ultramafic catchment soils during extended periods of inferred drying showed associations with dark septate endophytes (Ploettnerulaceae and Didymellaceae) that can produce large quantities of siderophores to solubilize mineral-bound ferrous iron, releasing bioavailable ferrous iron needed for several processes in plants, including photosynthesis. Our study showed that sedaDNA metabarcoding paired with the analysis of geochemical parameters yielded plausible insights into fungal-plant-soil interactions, and inferred changes in the paleohydrology and catchment evolution of tropical Lake Towuti, spanning more than one Myr of deposition. Full article
(This article belongs to the Special Issue Ancient Microbiomes in the Environment)
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