Detection of microbial biomass in subseafloor sediment by pyrolysis⿿GC/MS

Abstract

The conventional approaches for qualitative and quantitative assessment of microbial biomass in sediments, e.g. via quantitative polymerase chain reaction or intact polar lipids analysis, are rather tedious and time-consuming. Here we present a new, optimized and simple pyrolysis-gas chromatography/mass spectrometry protocol for rapid screening of sediment samples for the presence of microbial signals and quantification of bulk population.Analysis of microbial cultures of different bacterial and archaeal lineages as well as reference substances and model compounds provided molecular fingerprints for tracking microbial biomass. The diagnostic fingerprints consist of benzyl nitrile (derived from DNA and protein), 2-furanmethanol (from DNA and peptidoglycan), indole (from peptidoglycan and protein), phenol (from DNA, peptidoglycan and protein) and pyrrole (from peptidoglycan).Detection of microbial signals through the molecular fingerprints requires a cell density of at least 10 6 cells/g, whereas at least 10 7 cells/g is necessary for quantification. The pyrolysis method was applied to marine sediments from different depths (until ~ 400 m below the seafloor at the Canterbury Basin) and with different organic carbon contents (0.11-6.99%).

Expanding exploration of dynamic microplastic surface characteristics and interactions

“…It is possible that this method could be used to expand examination of accumulated biological factors; Py-GCMS has been used to this end previously. Zhu, et al [67] used Py-GCMS to quantify microbial biomass through the detection of specific "microbial signals"…”

Meta‐omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust

“…(2018) who found fungal gene expression associated with secretion of exoenzymes that break complex refractory compounds in marine sediments. Although necromass is thought to be a limited source of energy for microbial communities in marine sediments (Bradley et al ., 2018), other studies suggest necromass is a non‐trivial source of carbon and energy in deep subsurface habitats (Lomstein et al ., 2012; Jørgensen and Marshall, 2016; Zhu et al ., 2016; Braun et al ., 2017; Thomas et al ., 2019). Fungi can thus be seen as able to potentially recycle ‘their own’ or their dead neighbours in a cannibalistic way (Zinke et al ., 2019).…”

“…Since organic matter degradation is intensive in surficial sediment layers (Orcutt et al ., 2011b), deeper subsurface microbes may depend on pools of remaining refractory organic matter, necromass and delivery of nutrients by subsurface fluid flows (Jørgensen and Marshall, 2016). It was recently reported that deep subsurface allochtonous and autochtonous necromass may provide some fraction of the energy needs of deep biosphere microorganisms (Zhu et al ., 2016; Bradley et al ., 2018). Despite expected challenges for obtaining sufficient carbon and energy in this lithified realm, microbial chemoheterotrophs, including fungi, can survive.…”

Evaluating the effect of biochar addition on the anaerobic digestion of swine manure: application of Py-GC/MS

“…Other microbial pyrolysis products selected for tracking microbial signals, this case in sediments, are Benzyl nitrile, 2-furanmethanol, indole, phenol and pyrrole (Zhu et al 2016). In the present study, phenol and Indole were clearly discernible in all chromatograms.…”

“…Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) has been widely applied for the study of complex materials such as soil organic matter and recently for biomass characterisation (Liu et al 2016;Zhu et al 2016). The main advantages of the pyrolysis route for analysing complex organic samples are minimal sample preparation, minimum time of analysis and relative low cost (Prasad et al 2006).…”