Corrigendum to "An open-source, automated, gas sampling peripheral for laboratory incubation experiments using cavity ring-down spectroscopy" [HardwareX 10 (2021) e00208].

[This corrects the article DOI: 10.1016/j.ohx.2021.e00208.].

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate.

If biochar is to be used for carbon (C) management, we must understand how weathering or ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550°C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was accelerated via three different processes, namely, (a) physical ageing-subjecting biochar to alternating freeze-thaw and wet-dry cycles, (b) chemical ageing-treating biochar with concentrated hydrogen peroxide and (c) biological ageing-incubating biochar in the presence of nutrients and microorganisms. Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Biochar C mineralization between ageing treatments was significantly different in the case of 350°C biochar (p value = 0.03). Among the 350°C biochars, physical ageing resulted in the greatest increase (by 103%) in biochar C mineralization (p value = 0.05). However, in the case of 550°C biochar, ageing did not result in a significant change in biochar C mineralization (p value = 0.40). Biochar C mineralization was positively correlated with an increase in O/C ratio post-ageing (rs = 0.86, p value = 0.01). In the case of 350°C biochar, surface oxidation during ageing enhanced biochar degradation by the isolate. For 550°C biochar, however, ageing did not significantly increase biochar C mineralization, likely due to high condensed aromatic C content and lower surface oxidation during ageing. The results from our study suggest that low temperature aged biochar is more susceptible to biological degradation by soil microbes. These findings have implications for the use of biochar for long term C storage in soils.

Pyrolyzed Substrates Induce Aromatic Compound Metabolism in the Post-fire Fungus, Pyronema domesticum.

Wildfires represent a fundamental and profound disturbance in many ecosystems, and their frequency and severity are increasing in many regions of the world. Fire affects soil by removing carbon in the form of CO2 and transforming remaining surface carbon into pyrolyzed organic matter (PyOM). Fires also generate substantial necromass at depths where the heat kills soil organisms but does not catalyze the formation of PyOM. Pyronema species strongly dominate soil fungal communities within weeks to months after fire. However, the carbon pool (i.e., necromass or PyOM) that fuels their rise in abundance is unknown. We used a Pyronema domesticum isolate from the catastrophic 2013 Rim Fire (CA, United States) to ask whether P. domesticum is capable of metabolizing PyOM. Pyronema domesticum grew readily on agar media where the sole carbon source was PyOM (specifically, pine wood PyOM produced at 750°C). Using RNAseq, we investigated the response of P. domesticum to PyOM and observed a comprehensive induction of genes involved in the metabolism and mineralization of aromatic compounds, typical of those found in PyOM. Lastly, we used 13C-labeled 750°C PyOM to demonstrate that P. domesticum is capable of mineralizing PyOM to CO2. Collectively, our results indicate a robust potential for P. domesticum to liberate carbon from PyOM in post-fire ecosystems and return it to the bioavailable carbon pool.

An open-source, automated, gas sampling peripheral for laboratory incubation experiments using cavity ring-down spectroscopy.

Spectroscopic instruments are becoming increasingly popular for measuring the isotopic composition and fluxes of a wide variety of gases in both field and laboratory experiments. The popularity of these instruments has created a need for automated multiplexers compatible with the equipment. While there are several such peripherals commercially available, they are currently limited to only a small number of samples (≤16), which is insufficient for some studies. To support researchers in constructing custom, larger-scale systems, we present our design for a scalable gas sampling peripheral that can be programmed to autonomously sample up to 56 vessels - the "multiplexer". While originally designed to be used with a Picarro cavity ring-down spectroscopy (CRDS) system, the multiplexer design and data processing approach implemented can be easily adapted to serve as a gas sampling/delivery platform for a wide variety of instruments including other cavity ring-down systems and infra-red gas analyzers. We demonstrate the basic capabilities of the multiplexer by using it to autonomously sample head-space CO2 from 14 laboratory-incubated soils amended with 13C-enriched pyrogenic organic matter for analysis in a Picarro G2201-i cavity ring-down spectroscopy system.

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

Degradation and Microbial Uptake of C60 Fullerols in Contrasting Agricultural Soils.

The environmental fate of functionalized carbon nanomaterials (CNM) remains poorly understood. Using 13C-labeled nanomaterial we present the results of a study investigating the mineralization and microbial uptake of surface-functionalized C60 (fullerols) in agricultural soils with contrasting properties. Soil microcosms rapidly mineralized fullerol C, as determined by 13C-content in the respired CO2, with higher fullerol mineralization in an organic, clay-rich soil versus a silty, low C soil (∼56.3% vs ∼30.9% fullerol C mineralized over 65 days). By tracking the enriched 13C from fullerol into microbial phospholipid fatty acids (PLFA) we also report, for the first time, the incorporation of nanomaterial-derived C into soil microbial biomass, primarily by fungi and Gram-negative bacteria. While more fullerol C was incorporated into PLFA in the organic C-rich soil (0.77% vs 0.19% of PLFA C), this soil incorporated fullerol C into biomass less efficiently than the silty, low C soil (0.13% and 0.84% of assimilated fullerol C, respectively). These results demonstrate that, in contrast to pristine C60, surface functionalized C60 are unlikely to accumulate in surface soils and are readily mineralized by a range of soil microorganisms.

Soil microbial response to photo-degraded C60 fullerenes.

Recent studies indicate that while unfunctionalized carbon nanomaterials (CNMs) exhibit very low decomposition rates in soils, even minor surface functionalization (e.g., as a result of photochemical weathering) may accelerate microbial decay. We present results from a C60 fullerene-soil incubation study designed to investigate the potential links between photochemical and microbial degradation of photo-irradiated C60. Irradiating aqueous (13)C-labeled C60 with solar-wavelength light resulted in a complex mixture of intermediate products with decreased aromaticity. Although addition of irradiated C60 to soil microcosms had little effect on net soil respiration, excess (13)C in the respired CO2 demonstrates that photo-irradiating C60 enhanced its degradation in soil, with ∼ 0.78% of 60 day photo-irradiated C60 mineralized. Community analysis by DGGE found that soil microbial community structure was altered and depended on the photo-treatment duration. These findings demonstrate how abiotic and biotic transformation processes can couple to influence degradation of CNMs in the natural environment.

Weathering of pyrogenic organic matter induces fungal oxidative enzyme response in single culture inoculation experiments.

The addition of pyrogenic organic matter (PyOM), the aromatic carbon-rich product of the incomplete combustion of plant biomass or fossil fuels, to soil can influence the rate of microbial metabolism of native soil carbon. The interaction of soil heterotrophs with PyOM may be governed by the surficial chemical and physical properties of PyOM that evolve with environmental exposure. We present results of a 36-day laboratory incubation investigating the interaction of a common white-rot fungus, Trametes versicolor, with three forms of 13C-enriched (2.08 atom% 13C) PyOM derived from Pinus ponderosa (450 °C): one freshly produced, and two artificially weathered (254 nm, UV light-water treatment and water-leaching alone). Analysis (FTIR, XPS) of the UV-weathered PyOM showed increased aliphatic C-H content and oxidation of aromatic carbon relative to both the original and water-leached PyOM. The addition of both weathered forms of PyOM stimulated (positively primed) fungal respiration of the growth media, while the unaltered PyOM mildly inhibited (negatively primed) respiration. Artificial weathering resulted in higher oxidative (laccase and peroxidase) enzyme activity than unaltered PyOM, possibly the result of a diminished capacity to bind reactive substrates and extracellular enzymes after weathering. However, and contrary to expectations, simple water-leached weathering resulted in a relatively higher enzyme activity and respiration than that of UV-weathering. The 13C content of respired CO2 indicated negligible fungal oxidation of PyOM for all treatments, demonstrating the overall low microbial reactivity of this high temperature PyOM. The increased enzymatic and positive priming response of T. versicolor to weathered PyOM highlights the importance of weathering-induced chemistry in controlling PyOM-microbe-soil carbon interactions.

Oxidative enzymatic response of white-rot fungi to single-walled carbon nanotubes.

Although carbon nanomaterials such as single-walled carbon nanotubes (SWCNT) are becoming increasingly prevalent in manufacturing, there is little knowledge on the environmental fate of these materials. Environmental degradation of SWCNT is hindered by their highly condensed aromatic structure as well as the size and aspect ratio, which prevents intracellular degradation and limits microbial decomposition to extracellular processes such as those catalyzed by oxidative enzymes. This study investigates the peroxidase and laccase enzymatic response of the saprotrophic white-rot fungi Trametes versicolor and Phlebia tremellosa when exposed to SWCNTs of different purity and surface chemistry under different growth conditions. Both unpurified, metal catalyst-rich SWCNT and purified, carboxylated SWCNTs promoted significant changes in the oxidative enzyme activity of the fungi while pristine SWCNT did not. These results suggest that functionalization of purified SWCNT is essential to up regulate enzymes that may be capable of decomposing CNT in the environment.