Influence of Methanogenic Populations in Holocene Lacustrine Sediments Revealed by Clone Libraries and Fatty Acid Biogeochemistry

Vuillemin, Aurèle; Ariztegui, Daniel; Nobbe, G. H.; Schubert, Carsten J.

doi:10.1080/01490451.2013.824050

Cited by 13 publications

(16 citation statements)

References 82 publications

(113 reference statements)

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“…Detailed procedures for DNA extraction, PCR amplification and denaturing gradient gel electrophoresis (DGGE) were published elsewhere (Vuillemin et al, 2013a(Vuillemin et al, , 2014b. In brief, total DNA was extracted from sediment samples using the commercial Mobio PowerSoil Isolation kit.…”

Section: Clone Library and Phylogenetic Analysismentioning

confidence: 99%

Recording of climate and diagenesis through sedimentary DNA and fossil pigments at Laguna Potrok Aike, Argentina

et al. 2016

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Abstract. Aquatic sediments record past climatic conditions while providing a wide range of ecological niches for microorganisms. In theory, benthic microbial community composition should depend on environmental features and geochemical conditions of surrounding sediments, as well as ontogeny of the subsurface environment as sediment degraded. In principle, DNA in sediments should be composed of ancient and extant microbial elements persisting at different degrees of preservation, although to date few studies have quantified the relative influence of each factor in regulating final composition of total sedimentary DNA assemblage. Here geomicrobiological and phylogenetic analyses of a Patagonian maar lake were used to indicate that the different sedimentary microbial assemblages derive from specific lacustrine regimes during defined climatic periods. Two climatic intervals (Mid-Holocene, 5 ka BP; Last Glacial Maximum, 25 ka BP) whose sediments harbored active microbial populations were sampled for a comparative environmental study based on fossil pigments and 16S rRNA gene sequences. The genetic assemblage recovered from the Holocene record revealed a microbial community displaying metabolic complementarities that allowed prolonged degradation of organic matter to methane. The series of Archaea identified throughout the Holocene record indicated an age-related stratification of these populations brought on by environmental selection during early diagenesis. These characteristics were associated with sediments resulting from endorheic lake conditions and stable pelagic regime, high evaporative stress and concomitant high algal productivity. In contrast, sulphate-reducing bacteria and lithotrophic Archaea were predominant in sediments dated from the Last Glacial Maximum, in which pelagic clays alternated with fine volcanic material characteristic of a lake level highstand and freshwater conditions, but reduced water column productivity. Comparison of sedimentary DNA composition with that of fossil pigments suggested that post-depositional diagenesis resulted in a rapid change in the initial nucleic acid composition and overprint of phototrophic communities by heterotrophic assemblages with preserved pigment compositions. Long DNA sequences (1400–900 bp) appeared to derive from intact bacterial cells, whereas short fragments (290–150 bp) reflected extracellular DNA accumulation in ancient sediments. We conclude that sedimentary DNA obtained from lacustrine deposits provides essential genetic information to complement paleoenvironmental indicators and trace post-depositional diagenetic processes over tens of millennia. However, it remains difficult to estimate the time lag between original deposition of lacustrine sediments and establishment of the final composition of the sedimentary DNA assemblage.

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Section: Clone Library and Phylogenetic Analysismentioning

confidence: 99%

Recording of climate and diagenesis through sedimentary DNA and fossil pigments at Laguna Potrok Aike, Argentina

et al. 2016

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“…In ancient records, it is often best preserved within intact resting stages (Domaizon et al, 2017), such as pollens, planktonic cysts or endospores, which can then be used to trace past environmental changes (Coolen and Overmann, 1998, 2007; Parducci et al, 2005; Coolen et al, 2013) and complement other molecular indicators (Coolen et al, 2008, 2009; Boere et al, 2009; Vuillemin et al, 2014b, 2016a). However, persistent activity of microorganisms in sediments also alters this record due to selective preservation of previous assemblages (Boere et al, 2011a,b).…”

Section: Introductionmentioning

confidence: 99%

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

et al. 2017

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Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.

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“…5 and 6) indicated gradual evolution of the assemblages within the uppermost 10 m of sediment. For example, the predominant methanogen varied with depth from Methanolinea to Methanosarcina and Methanoregula (Vuillemin et al, 2014b). Marine-related sequences also shifted from Group 1 to Benthic Group B and then Benthic Group D before disappearing below 5 m depth.…”

Section: Preservation and Interpretation Of Fossil Dnamentioning

confidence: 97%

“…18361 First, at 5 m depth (ca. 5 ka BP), 16S rRNA gene sequences revealed a predominantly active microbial assemblage capable of on-site methane production during OM degradation (Wüst et al, 2009;Vuillemin et al, 2014b) during an interval of subsaline and productive lake conditions (Fig. 2).…”

Section: Preservation and Interpretation Of Fossil Dnamentioning

confidence: 98%

Recording of climate and diagenesis through fossil pigments and sedimentary DNA at Laguna Potrok Aike, Argentina

Vuillemin

Ariztegui

Leavitt

et al. 2015

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Abstract. Aquatic sediments record past climatic conditions while providing a wide range of ecological niches for microorganisms. Although marine sedimentary microbial assemblages are often defined by their surrounding geochemical conditions, the influence of environmental features upon microbial development and post-depositional survival remains largely unknown in the lacustrine realm. Due to long-term microbial activity, the composition of environmental DNA can be expected to evolve with sediment depth and over time and therefore should reflect both ancient and extant microbial populations, but this hypothesis has rarely been tested using a multiproxy approach. Here geomicrobiological and phylogenetic analyses of a Patagonian maar lake were used to indicate that the different sedimentary microbial assemblages derive from specific lacustrine regimes during defined climatic periods. Two well defined climatic intervals whose sediments harboured active microbial populations and measurable ATP were sampled for a comparative environmental study based on fossil pigments and 16S rRNA gene sequences. Bacterial and archaeal 16S rRNA gene sequences recovered from the Holocene record revealed a microbial community adapted to subsaline conditions actively producing methane during organic matter degradation. These characteristics were associated with sediments resulting from endorheic lake conditions with high evaporative stress and concomitant high algal productivity. Moreover, archaeal clone libraries established throughout the Holocene record indicate an age-related stratification of these populations, consistent with a gradual use of organic substrates after deposition. In contrast, sulphate-reducing bacteria and lithotrophic Archaea were predominant in sediments dated from the Last Glacial Maximum, in which pelagic clays alternated with fine volcanic material characteristic of a lake level highstand and freshwater conditions, but reduced water column productivity. These patterns reveal that microbial assemblages identified from environmental DNA stemmed from a variety of sedimentary niches associated with climate-dependent factors (catchment inflows, water column conditions, productivity), but that initial assemblages underwent structural changes and selective preservation during early diagenesis to result in the final composition entombed in the sediments. We conclude that environmental DNA obtained from lacustrine sediments provides essential genetic information to complement paleoenvironmental indicators and trace climate change and post-depositional diagenetic processes over tens of millennia.

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Influence of Methanogenic Populations in Holocene Lacustrine Sediments Revealed by Clone Libraries and Fatty Acid Biogeochemistry

Cited by 13 publications

References 82 publications

Recording of climate and diagenesis through sedimentary DNA and fossil pigments at Laguna Potrok Aike, Argentina

Recording of climate and diagenesis through sedimentary DNA and fossil pigments at Laguna Potrok Aike, Argentina

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

Recording of climate and diagenesis through fossil pigments and sedimentary DNA at Laguna Potrok Aike, Argentina

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