Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Abstract

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

“…Microbial communities within natural environments carry out a plethora of functions essential for nutrient cycling, organic matter decomposition, and ecosystem stability (Tiquia et al, 2006a,b;Tiquia, 2008Tiquia, , 2010bIgisu et al, 2012;Mckindles and Tiquia-Arashiro, 2012;Flood et al, 2015;Tiquia-Arashiro and Grube, 2019;Duncan and Petrou, 2022;Naylor et al, 2022). The metabolic activities and functional profiles of the microbial communities are influenced by environmental factors, including temperature fluctuations, nutrient availability, and pollutant exposure (Liu et al, 2003;Wu et al, 2005;Gentile et al, 2006;Tiquia, 2010aTiquia, , 2011Dong et al, 2017;Qin et al, 2018;Tiquia-Arashiro, 2019b;Huang et al, 2020;Cabugao et al, 2022;Duncan and Petrou, 2022).…”

Reviews in astronomy and space sciences

“…Most geomicrobiological subsurface information can be generated using different conventional analytical methodologies (for a recent description of most of these methodologies in hard rock deep subsurface drilling see Amils et al, 2023): Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and Total Reflection X-Ray Fluorescence (TXRF) for elemental analysis of the solid substrate and the bioavailable elements; X-Ray Diffraction (XRD) for the mineral composition of the substrate; Scanning Electron Microscopy (SEM) for the visualization of mineral-microbe interactions; Confocal Raman Spectroscopy to evaluate mineralmicrobe interaction (Escudero et al, 2020); Isotope Ratio Mass Spectrometry for identification of the involved metabolisms (Cabugao et al, 2022); ionic and gas chromatography for the analysis of substrates and products from different metabolisms; 16S rRNA gene cloning, 16S rRNA gene amplicon and metagenomic shotgun sequencing (Puente- Sánchez et al, 2018), immunological detection, FISH, Catalysed Reported Deposition Fluorescence in situ Hybridization (CARD-FISH), and lipid biomarker analysis for complementary evaluation of microbial diversity, each one with its own limitations; enrichment cultures, metatranscriptomics , quantitative PCR (Jesser et al, 2015) metaproteomics (Bagnoud et al, 2016), single cell genomics (Becraft et al, 2021) and Time-of-flight Secondary Ionization Mass Spectrometry (Tof-SIMS) (Viang and Dong, 2012) for identification of specific metabolisms; isolation of microorganisms for phenotypic characterization; genome sequencing and gene annotation for the identification of potential metabolisms. The use of several complementary methodologies is strongly recommended to identify convergent results avoiding the bias introduced by each one (Amils et al, 2023).…”

Assessing the substrate specificity of a micropollutant degrading strain: generalist or specialist?

“…Combining results from pure substrate studies with continued research conducting advanced characterization of environmental DOM, using for example uorescence spectroscopy, high resolution mass spectrometry, and NMR techniques, 16,31,50,51,52 might further elucidate the role of specic DOM fractions for the growth of OMP degraders under complex environmental conditions. In particular working with high resolution mass spectrometry would further allow to study OMP and DOM biodegradability in the ng L −1 -mg L −1 range.…”