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Abstract Low molecular weight organic compounds (LMWOC) represent a small but critical component of soil organic matter (SOM) for microbial growth and metabolism. The fate of these compounds is largely under microbial control, yet outside the cell, intrinsic soil properties can also significantly influence their turnover and retention. Using a chronosequence representing 1200 ka of pedogenic development, we compared physicochemical vs biological controls on the turnover and retention of fast-cycling carbon (C), e.g. glucose (GLU) and p -hydroxybenzoic acid (PHBA). Along the chronosequence, we observed mineralogical gradients whereby amorphous constituents were greatest in intermediate-aged sites, while older sites demonstrated soils with more ordered and less reactive mineralogy. Soil microbial community composition varied along the soil chronosequence and we observed reductions in total biomass and fungal biomass from younger to older sites, but this did not affect the turnover of LMWOC. Microbial utilization of LMWOC was substrate- and soil-dependent; amorphous Fe and Al oxides reduced the respiration of PHBA but respiration from glucose remained less affected. Variation in soil mineralogy did not significantly alter recovery of PHBA within microbial biomass or fungal vs. bacterial biomarkers, suggesting that reduced respiration of the phenolic resulted from direct mineral interaction with ionizable functional groups rather than changes to microbial allocation of PHBA. We conclude patterns of soil carbon storage observed across chronosequences are moderated by mineralogical effects on microbial access to LMWOC, independent of variation in microbial community composition. Graphical abstract Along the Cowlitz River soil chronosequence (∼1200 ka) clear chronological transformations in mineralogical (e.g., pedogenic Fe and Al) and textural properties result in a gradient of surface soils with comparatively higher abundance of amorphous constituents (active Fe and Al) among intermediate-aged sites, and more ordered and less reactive mineralogy (crystalline Fe oxide) among older sites. Soil microbial community composition varied (depicted as different color and constituency in the graphic) with soil mineralogy and texture, but this had little effect on the turnover of low molecular weight organic compounds (LMWOC). Patterns of soil carbon (C) storage observed across the chronosequence are moderated by mineralogical effects on microbial access to LMWOC, independent of variation in microbial community composition. Metabolization of glucose to CO 2 was low (high C assimilation efficiency) regardless of edaphic properties. In contrast, p -hydroxybenzoic acid, a substrate with variable charge capacity, and typically lower C assimilation efficiency, demonstrated reduced metabolization to CO 2 among soils with higher active Fe and Al. Presumably this is due to direct mineral interaction with ionizable functional groups as opposed to variation in microbial allocation of p -hydroxybenzoic acid. Image 1 Highlights • The Cowlitz River soil chronosequence represents 1200 ka of pedogenic development. • We examined relationships between soil mineralogy, microbes, and rates of C turnover. • Microbial community composition, but not functionality varies with soil age. • Soil mineralogy (especially Al and Fe chemistry) moderates microbial access to LMWOC. • Internal allocation of LMWOC to microbial products drives short-term C retention. [ABSTRACT FROM AUTHOR]

Abstract: Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2 gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the direct (microaerobiosis) and indirect (loss of plant C inputs) effects of elevated soil CO2 flux have significant impacts on the composition and overall structural trajectory of soil microbial populations within disturbed areas. [Copyright &y& Elsevier]

The productivity of temperate forests is often limited by soil N availability, suggesting that elevated atmospheric N deposition could increase ecosystem C storage. However, the magnitude of this increase is dependent on rates of soil organic matter formation as well as rates of plant production. Nonetheless, we have a limited understanding of the potential for atmospheric N deposition to alter microbial activity in soil, and hence rates of soil organic matter formation. Because high levels of inorganic N suppress lignin oxidation by white rot basidiomycetes and generally enhance cellulose hydrolysis, we hypothesized that atmospheric N deposition would alter microbial decomposition in a manner that was consistent with changes in enzyme activity and shift decomposition from fungi to less efficient bacteria. To test our idea, we experimentally manipulated atmospheric N deposition (0, 30 and 80 kg NO3−-N) in three northern temperate forests (black oak/white oak (BOWO), sugar maple/red oak (SMRO), and sugar maple/basswood (SMBW)). After one year, we measured the activity of ligninolytic and cellulolytic soil enzymes, and traced the fate of lignin and cellulose breakdown products (13C-vanillin, catechol and cellobiose). In the BOWO ecosystem, the highest level of N deposition tended to reduce phenol oxidase activity (131±13 versus 104±5 μmol h−1 g−1) and peroxidase activity (210±26 versus 190±21 μmol h−1 g−1) and it reduced 13C-vanillin and 13C-catechol degradation and the incorporation of 13C into fungal phospholipids (p<0.05). Conversely, in the SMRO and SMBW ecosystems, N deposition tended to increase phenol oxidase and peroxidase activities and increased vanillin and catechol degradation and the incorporation of isotope into fungal phospholipids (p<0.05). We observed no effect of experimental N deposition on the degradation of 13C-cellulose, although cellulase activity showed a small and marginally significant increase (p<0.10). The ecosystem-specific response of microbial activity and soil C cycling to experimental N addition indicates that accurate prediction of soil C storage requires a better understanding of the physiological response of microbial communities to atmospheric N deposition. [Copyright &y& Elsevier]

Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. [Copyright &y& Elsevier]

Soil organic matter (SOM) improves soil fertility and mitigates disturbance related to climate and land use change. Microbial necromass (the accumulated cellular residues of microorganisms) comprises the majority of soil C, yet the formation and persistence of necromass in relation to mineralogy is poorly understood. We tested whether soil minerals had different microbial necromass association mechanisms. Specifically, we tested whether microbial necromass directly sorbed to mineral surfaces or was consumed by live microorganisms prior to mineral association. Applying Raman microspectroscopy with 13C enriched microbial necromass to quantify microbe-mineral interactions, we show that mineralogy alters the initial mechanism of microbial necromass association. In the presence of K-feldspar (lower abiotic C preservation potential), microbial necromass required assimilation by live microorganisms for mineral retention. In contrast, with amorphous aluminum hydroxide (higher abiotic C preservation potential) microbial necromass was retained predominately through abiotic sorption, and was subsequently protected from microbial decomposition. Despite different mechanisms, both minerals retained similar quantities of microbial necromass under biotic conditions. Mineralogy determined not only the quantity of mineral-associated C, but the distinct pathway of microbial necromass association. These findings show the utility of Raman microspectroscopy as a technique to study microbe-mineral interactions, and imply that heterogeneity in mineral-organic interactions could result in gradients of organic matter stability. [ABSTRACT FROM AUTHOR]

Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO 2 and CH 4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH 4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function. [ABSTRACT FROM AUTHOR]

Though primary sources of carbon (C) to soil are plant inputs (e.g., rhizodeposits), the role of microorganisms as mediators of soil organic carbon (SOC) retention is increasingly recognized. Yet, insufficient knowledge of sub-soil processes complicates attempts to describe microbial-driven C cycling at depth as most studies of microbial-mineral-C interactions focus on surface horizons. We leveraged a well-studied paleo-marine terrace (90 ka) located near Santa Cruz, CA, to characterize the short-term (days to weeks) and intermediate-term (months to years) fate of two low molecular weight organic carbon. compounds at three depths in the soil profile (∼25 cm, A horizon; ∼75 cm A/B transition; and ∼125 cm, B horizon). We employed isotopically-labeled glucose (GLU) and oxalic acid (OXA) to represent two common classes of rhizodeposits: carbohydrates and organic acids. Using a combination of laboratory (9 d) and field (490 d) incubations, we traced the fate of GLU-C and OXA-C through dissolved-, metal-associated-, and microbially-respired CO 2 and bulk SOC pools. Our results suggest new SOC retention (i.e., defined as 13C label identified in solid or aqueous fractions) over intermediate time frames (490 d) is correlated with patterns in short-term (9 d) cycling dynamics, which in turn is related to the theoretical efficiency by which microorganisms process each substrate. For all horizons (A, A/B, and B) GLU-C was converted to CO 2 more quickly than OXA-C with modeled decomposition rates ∼2–4 times faster for GLU depending on microbial density (higher in A than B horizon). The faster decomposition rates of GLU-C increased fractional recovery (0.399 ± 0.026 to 0.504 ± 0.030 for GLU-C) compared to OXA-C (0.035 ± 0.003 to 0.127 ± 0.010) among all horizons in our field experiment (490 d). Though the overall proportion of GLU-C recovered in solid fractions did not vary significantly with horizon, based on 13C recovered in aqueous fractions the apparent mechanism for retention did. After the 9-d laboratory incubation, fractional recovery for GLU-C among C pools associated with microbial biomass was almost 20× higher than OXA-C (0.192 versus 0.010, respectively across all horizons). More than a year later, 43–46% of GLU-C retained in the field incubation was extractable with a neutral salt (representing a pool of soil C residing within or available to microbial biomass) among A and A/B horizons, while only 6% of retained GLU-C was similarly extractable in the B horizon. Thus, it appears among depths with higher microbial density (A, A/B horizons), anabolic recycling is the most likely process contributing to the persistence of glucose C, whereas abiotic sinks contributed more to intermediate-term stability for GLU-C in the B horizon. By contrast, most OXA-C was lost, presumably as CO 2 , over the short-term from the A and A/B horizons (fractional recovery: 0.136 ± 0.011 and 0.091 ± 0.002, respectively). However, though substantially lower than GLU-C recovered at the conclusion of our field experiment, the fraction of oxalic acid C retained in the B horizon over both short- (0.72 ± 0.037) and intermediate-time (0.127 ± 0.010) frames was several-fold higher than for overlying horizons. The specific process(es) (e.g., more efficient microbial utilization, metal-organic complexation, direct adsorption to the mineral matrix, etc.) contributing to higher retention for OXA-C at depth are discussed but remain unresolved. We examined the cycling of two different isotopically labeled low molecular weight organic carbon (LMWOC) compounds, glucose (red) and oxalic acid (blue), using a combination of field and laboratory incubations. Our results suggest that in surface soils, glucose was retained to a greater extent, likely through microbial reassimilation of necromass, compared to oxalic acid, which was largely lost through mineralization to CO 2. In the subsurface soils, mechanisms including organo-metal complexation (hexagons) and other unidentified mineral organic associations allowed for greater abiotic retention of both carbon compounds. Though, there was still evidence of greater glucose recycling and oxalic acid mineralization at depth. [Display omitted] • Glucose and oxalic acid C traced over 9 and 490 d through A, A/B, B soil horizons. • After 490 d in situ approximately half of glucose C was retained among all horizons. • Anabolism appears to contribute to persistence of glucose C at all depths. • Oxalic acid C poorly retained among A, A/B soil horizons; more persistent at depth. • Importance of organo-metal complexation appears to increase with depth for newer OC. [ABSTRACT FROM AUTHOR]