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Pyrogenic carbon (PyC), the product of incomplete biomass combustion, is a key component of soil organic carbon (SOC) because it can persist in soils for centuries to millennia. Quantifying PyC across large spatial scales remains a significant challenge in constraining the global carbon cycle. We measured PyC in topsoils across Europe using molecular marker (benzene polycarboxylic acids, BPCA) and spectroscopic techniques (Diffuse Reflectance Infrared Fourier Transform Spectroscopy, DRIFTS). We developed a calibration between BPCA and DRIFTS, but the calibration was less reliable (Y-variance explained = 0.62) than previous reports due to low soil PyC content and heterogeneity of soil matrices. Thus, we performed multiple regressions to identify drivers of PyC distribution using only the measured BPCA data. PyC content varied widely among soils, contributing 0–24% of SOC. Organic carbon was the strongest predictor of soil PyC content, but mean annual temperature, clay, and cation exchange capacity also emerged as predictors. PyC contributes a smaller proportion of SOC in European soils compared to other geographic regions. Comparing soil PyC measurements to PyC production rates in high latitude and Mediterranean regions suggests that transport, degradation, and recombustion are important mechanisms regulating soil PyC accumulation.

A 2,4-dichlorophenoxyactic acid (2,4-D)-resistant population of

Mycobacterial lipoarabinomannan (LAM) is in an essential cell envelope lipopolysaccharide anchored both to the plasma and outer membranes. To understand critical biological questions such as the biosynthesis, spatial organization of LAM within the cell envelope, structural remodeling during growth, and display or lack of display of LAM-based antigenicity requires a basic understanding of the primary structure of the mannan, arabinan and how they are attached to each other. Herein, using enzymatic digestions and high-resolution mass spectrometry, we show that the arabinan component of LAM is attached at the non-reducing end of the mannan rather than to internal regions. Further, we show the presence of secondary extended mannan side chains attached to the internal mannan region. Such findings lead to a significant revision of the structure of LAM and lead to guidance of biosynthetic studies and to hypotheses of the role of LAM both in the periplasm and outside the cell as a fundamental part of the dynamic mycobacterial cell envelope. Lipoarabinomannan is a carbohydrate expressed on mycobacterial cell surfaces and implicated in host-pathogen interactions, but its structure is not well-characterised. Here mass spectrometry studies of enzymatic digests reveal the presence of secondary extended mannan pendants and indicate a revised structure for the connectivity of the core domains.

Mycobacterium tuberculosis lipoarabinomannan (LAM) is a biomarker for active tuberculosis (TB) disease. The presence of LAM in the urine of TB patients, whether HIV positive or negative, has been validated by a gas chromatography/mass spectral method with good specificity (84%) and sensitivity (99%). However, point-of-care (POC) methods to detect TB LAM in urine using immunoassays have poor sensitivity and are limited to only HIV coinfected TB diagnosis. We hypothesized that these disappointing results with the POC methods may be due to the antibodies used in the immunoassays as there could be structural differences between LAM in vivo and LAM in vitro. To address this issue, we infected C3HeB/FeJ mice with M.tb W. Beijing SA161 and purified LAM from the lung. Analysis of these sources of LAM using a panel of existing mAbs revealed differences in epitope patterns. Conventionally, the non-reducing termini of LAM are identified by their release with endoarabinanase. These epitopes correspond to linear tetra-(Ara4), branched hexa-(Ara6) arabinofuranosides, and their mannose-capped versions. We discovered two distinct epitopes. In the first case, it was found that the non-reducing termini of LAM from M.tb strain SA161 are highly succinylated, especially when the LAM was isolated from the mouse lungs. In the second case, it was found that Cellulomonas endoarabinanase digestion of LAM from both SA161 and LAM from a TB+ HIV- patient's urine yielded epitopes based on 5 arabinoses as major components and a profound lack of Ara6. The epitopes based on 5 arabinoses from M.tb SA161 and from the LAM in human urine must result from underlying structural and thus epitope differences. These results suggest approaches to develop specific antibodies for POC tests for LAM in the urine of suspected TB patients.

As glaciers in the western United States thaw in response to warming, they release dissolved organic matter (DOM) to alpine lakes and streams. Biological availability of DOM from small mountain glaciers is unknown. Differences in DOM bioavailability between glacier types like rock and ice glaciers remains undefined, yet rock glaciers outnumber ice glacier approximately ten to one at low latitudes. To assess which components of aquatic DOM are most reactive and the potential for glacial DOM from low latitude glaciers to subsidize heterotrophy in alpine headwaters we evaluated reactivity and molecular composition of DOM from ice glaciers and rock glaciers from four paired catchments (each with a glacier and rock glacier at their headwaters). Biological reactivity was linked to molecular composition by evaluating the chemical characteristics of each DOM pool pre- and post-incubation using common microbial community laboratory assays paired with untargeted mass spectrometry-based metabolomics. Glacier and rock glacier DOM was similar in concentration and chemodiversity, but differed in composition. When incubated with a common microbial community, DOM from ice glacier meltwaters contained a higher proportion of bioavailable DOM (BDOM), and resulted in greater bacterial growth efficiency. Differences in DOM reactivity between glacier types was determined by differences in the relative abundance of only a few dozen compounds. Though BDOM was lower in rock glaciers, because rock glaciers are more abundant and are expected to have greater longevity, we propose that both glacial types will be important sources of bioavailable DOM to alpine headwaters over the coming years to decades.

Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource–diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

Nitrogen deposition from anthropogenic sources is a global problem that reaches even the most remote ecosystems. Responses belowground vary by ecosystem, and have feedbacks to geochemical processes, including carbon storage. A long-term nitrogen addition study in a subalpine forest has shown carbon loss over time, atypical for a forest ecosystem. Loss of microbial biomass is likely linked to lower soil carbon, but the mechanism behind this is still unknown. One possible explanation is through increased turnover due to grazing by soil fauna. Because nematodes occupy many trophic levels and are sensitive to trophic and environmental changes, assessing their communities helps reveal belowground responses. In this study, we tested the hypothesis that long-term nitrogen fertilization affects nematode community structure and maturity beneath coniferous forests in the Rocky Mountains, indicating a faster cycling, bacterial-driven system. We identified and enumerated nematodes by trophic group and family from experimental plots. Total nematode abundance was 40–96% greater in fertilized plots compared to the control, but richness, diversity, and ecological maturity were lower. The differences in abundance were driven by opportunistic bacterivores (e.g., Rhabditidae) and plant parasites (e.g., Tylenchidae), which made up 23 and 13% of the community in fertilized compared to 7 and 5% in control plots, respectively. Nematode maturity indices showed that the nematode food web was enriched (indicating high nutrient/resource status) and structured (all trophic levels present, including long-lived predators) in both treatments, but significantly more enriched in the fertilized treatment. Nonmetric multidimensional scaling of the relative abundance of nematode families demonstrated that nematode community composition differed between treatments, driven largely by opportunistic bacterivores (e.g., Rhabditidae) in the fertilized plots. The mechanism of the aboveground–belowground link between nitrogen deposition and nematode community composition is likely through increased microbial turnover, and sustained high-quality food for microbial grazing nematodes.

Headwater forest ecosystems of the western U.S. generate a large portion of the dissolved organic matter (DOM) transported across North America. Land cover changes that alter forest structure and forest species composition affect the quantity and composition of DOM transferred to aquatic ecosystems. Clear-cut harvesting effects ~1% of the forest area of North America annually, leaving most forests in varying stages of successional regrowth, and the total area of old-growth forest decreasing. The consequences of this widespread management practice on watershed carbon cycling remain unknown. We investigated the role of land cover change from old-growth subalpine forest to lodgepole pine dominated second-growth on the character and reactivity of DOM hillslope exports. We evaluated inputs of DOM from litter leachates and export of DOM collected at the base of trenched hillslopes during a three-year period (2016-2018) at the Fraser Experimental Forest in northcentral Colorado, USA. Dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were higher in lateral subsurface flow draining old- versus secondary-growth forest. Fluorescence spectroscopy showed that the DOM exported from the old-growth forest was more heterogeneous and aromatic and that proteinaceous, microbially processed DOM components were more prevalent in the second-growth forest. Biological oxygen demand (BOD) assays revealed much lower microbial metabolism of both DOM inputs from litter leachate and subsurface exports from old-growth forest. Old-growth and second-growth forests are co-mingled in managed ecosystems, and our findings demonstrate that the influence of species composition on DOM inputs can affect the reactivity of DOM transferred from terrestrial to aquatic ecosystems.

This double-blind study examined effects of a protease enzyme blend (Prohydrolase&reg, ) added to whey protein on post-resistance exercise aminoacidemia and intramuscular anabolic signaling were investigated in ten resistance-trained males. Participants completed 4 sets of 8&ndash, 10 repetitions in the leg press and leg extension exercises at 75% of 1-repetition maximum. Participants then consumed either 250 mg of Prohydrolase&reg, + 26 g of whey protein (PW), 26 g whey alone (W), or non-nutritive control (CON) in counterbalanced order. Blood samples were obtained prior to exercise (baseline) and then immediately-post (IP), 30-, 60-, 90-, 120-, and 180-min post-exercise. Muscle biopsies were taken at baseline, 1-h (1H), and 3-h (3H) post-exercise. Phosphorylation of AKTSer437 was decreased (3H only: p &lt, 0.001), mTORSer2448 was increased (1H: p = 0.025, 3H: p = 0.009), and p70S6KThr412 remained unchanged similarly for each condition. Plasma leucine, branch-chained amino acids, and essential amino acid concentrations for PW were significantly higher than CON (p &lt, 0.05) at 30 min and similar to W. Compared to IP, PW was the only treatment with elevated plasma leucine levels at 30 min (p = 0.007, ∆ = 57.8 mmol/L, 95% Confidence Interval (CI): 20.0, 95.6) and EAA levels at 180 min (p = 0.003, ∆ = 179.1 mmol/L, 95% CI: 77.5, 280.7). Area under the curve amino acid analysis revealed no differences between PW and W. While no different than W, these data indicate that PW was the only group to produce elevated amino acid concentrations 30-min and 180-min post-ingestion.

Mycobacteria synthesize intracellular, 6-O-methylglucose-containing lipopolysaccharides (mGLPs) proposed to modulate bacterial fatty acid metabolism. Recently, it has been shown that Mycobacterium tuberculosis mGLP specifically induces a specific subset of protective γ9δ2 T cells. Mild base treatment, which removes all the base-labile groups, reduces the specific activity of mGLP required for induction of these T cells, suggesting that acylation of the saccharide moieties is required for γ9δ2 T-cell activation. On the basis of this premise, we used analytical LC/MS and NMR methods to identify and locate the acyl functions on the mGLP saccharides. We found that mGLP is heterogeneous with respect to acyl functions and contains acetyl, isobutyryl, succinyl, and octanoyl groups and that all acylations in mGLP, except for succinyl and octanoyl residues, reside on the glucosyl residues immediately following the terminal 3-O-methylglucose. Our analyses also indicated that the octanoyl residue resides at position 2 of an internal glucose toward the reducing end. LC/MS analysis of the residual product obtained by digesting the mGLP with pancreatic α-amylase revealed that the product is an oligosaccharide terminated by α-(1→4)-linked 6-O-methyl-d-glucosyl residues. This oligosaccharide retained none of the acyl groups, except for the octanoyl group, and was unable to induce protective γ9δ2 T cells. This observation confirmed that mGLP induces γ9δ2 T cells and indicated that the acylated glucosyl residues at the nonreducing terminus of mGLP are required for this activity.

Drought is common in soil, yet its intensity and immediate effects vary with the timing of precipitation and the depth in the soil profile. We set out to analyze the patterns of soil C and N dynamics through the dry summer in a California annual grassland, and to analyze the processes that control those dynamics. During the dry season, inorganic N, soluble organic matter, and microbial biomass accumulated in soil. Concentrations were generally greater in the surface soil layer (0–10 cm) but increased in both surface and deeper soil (10–20 cm) over the course of the summer. There was a positive relationship between drought length, microbial biomass C and N, extractable C and N, and microbial activity upon rewetting. Upon rewetting of dry soils there was a pulse in nitrate availability (under field conditions) and, in the top 10 cm, a positive correlation between the initial CO2 pulse released upon rewetting and the drought length. In contrast, below 10 cm there was no correlation between the rewetting CO2 pulse and drought length. Soils from the top 10 cm and below 10 cm dried under controlled laboratory conditions showed the same CO2 pulse response to the length of drying as those in the field. These results suggest that the substrates that accumulate during the dry season are relatively labile, and that, in surface soils, biomass/substrate amounts and water availability control their persistence, while in deeper layers, some other factor is more important.

Summary It is becoming increasingly clear that plant roots can impact the decomposition of existing soil C in the rhizosphere. Studies under controlled conditions suggest this impact may be plant species dependent, but whether this is the case in natural conditions or what factors underlie this variation is mostly unknown. With a novel field-based isotopic approach combining 13C-enriched glucose and 5-bromo-2-deoxyuridine additions, we compared in situ C decomposition of added labile C and native soil C (priming) among eight semi-arid grassland species’ rhizospheres to investigate the factors driving inter-species variation. We examined the influence of several rhizosphere factors related to soil chemistry, microbial activity, microbial community, microbial stoichiometry, plant chemistry and root morphology. Plant species generated distinct microbial and chemical rhizosphere environments, which translated into differences in the direction, magnitude and temporal dynamics of the soil C priming. Soil C decomposition was positively related to soil C/P and soil N/P (via its influence on the bacterial community), which in turn were positively related to plant N/P. Plant C/N was also a significant factor via its negative influence on soil N/P. In contrast, the main direct predictors of labile C decomposition were microbial biomass, microbial C/N and the C-degrading enzymes, which in turn were linked to root morphology and C chemistry. Synthesis. Within this community, plant species’ rhizospheres can vary in their susceptibility to C loss in response to changes in C availability. Soil stoichiometry, driven by plant chemical traits, appeared to be the strongest driver of priming. Our study suggests that shifts in plant communities involving increases in N relative to P have the greatest potential to lead to C loss. We provide evidence of root morphology and C chemistry as drivers of labile C processing in soil, a novel empirical contribution to our understanding of the role of plant traits below-ground. The contrasting regulation of different pools of soil C suggests observations of the regulation of simple C compounds should not be extrapolated to the whole C pool. Our findings provide support for rhizosphere-driven mechanisms by which shifts in plant community composition could have implications on the ecosystem-level C balance.

Longleaf pine ( Pinus palustris Miller) forests in the southern United States are being restored and actively managed for a variety of goals including: forest products, biodiversity, C sequestration and forest resilience in the face of repeated disturbances from hurricanes and climate change. Managed southern pine forests can be sinks for atmospheric CO 2 in forest biomass; however, the persistence of biomass in the environment or in forest products is limited, thus making soil C the primary long-term pool. Little is known about the size of extant soil C pools, residence time of soil C or the role that frequent burning plays in C stabilization in longleaf pine ecosystems. We sampled soil from a chronosequence of longleaf pine stands ranging in age from 5 to 87 years to quantify the vertical distribution of soil organic carbon (SOC) stocks; both oxidizable (SOC OX ) and oxidation resistant (SOC R ) fractions, pyrogenic carbon (PyC) and the mean residence time (MRT) of SOC and its associated fractions. SOC stocks (0–1 m) ranged from 44.1 to 98.1 ( x ¯ = 77.0) Mg C ha −1 , and no effect of stand age or biomass accumulation on SOC stocks was detected. Soil C accumulation was associated with elevated clay and extractable Fe contents. While SOC concentration declined with soil depth, the proportion of SOC R in SOC increased with depth. PyC was a minor component of soil C, representing 5–7% of SOC and the proportion was not depth dependent. The MRT of SOC was hundreds of years near the surface and many thousands of years at depth. Though SOC R was less abundant than SOC OX , SOC R MRT was an order of magnitude greater than SOC OX MRT and had a strong influence on bulk SOC MRT. The majority of the PyC was in the less persistent SOC ox and not associated with long-term C storage in soil. Despite the flow of C from biomass in the form of decay products, litter fall, root turnover and pulses of PyC, these soils preserve little of recent inputs, which may be rapidly oxidized, lost to the atmosphere from periodic fires or, in the case of PyC, may be transported out of the system via erosion. Our results indicate that these soils were not strong sinks for atmospheric CO 2 , especially when compared to C accumulation in biomass.

Biogeochemical processing of dissolved organic matter (DOM) in headwater rivers regulates aquatic food web dynamics, water quality, and carbon storage. Although headwater rivers are critical sources of energy to downstream ecosystems, underlying mechanisms structuring DOM composition and reactivity are not well quantified. By pairing mass spectrometry and fluorescence spectroscopy, here we show that hydrology and river geomorphology interactively shape molecular patterns in DOM composition. River segments with a single channel flowing across the valley bottom export DOM with a similar chemical profile through time. In contrast, segments with multiple channels of flow store large volumes of water during peak flows, which they release downstream throughout the summer. As flows subside, losses of lateral floodplain connectivity significantly increase the heterogeneity of DOM exported downstream. By linking geomorphologic landscape-scale processes with microbial metabolism, we show DOM heterogeneity increases as a function of fluvial complexity, with implications for ecosystem function and watershed management., The underlying mechanisms structuring dissolved organic matter (DOM) composition and reactivity in rivers remain poorly quantified. Here, the authors pair mass spectrometry and fluorescence spectroscopy to show that hydrology and river geomorphology both shape molecular patterns in DOM composition.

We sought to determine if 28 days of probiotic supplementation influenced the plasma amino acid (AA) response to acute whey protein feeding. METHODS: Twenty-two recreationally active men (n = 11; 24.3 ± 3.2 yrs; 89.3 ± 7.2 kg) and women (n = 11; 23.0 ± 2.8 yrs; 70.2 ± 15.2 kg) participated in this double-blind, placebo-controlled, randomized study. Before (PRE) and after 28 days of supplementation (POST), participants reported to the lab following a 10-hr fast and provided a resting blood draw (0 min), then subsequently consumed 25 g of whey protein. Blood samples were collected at 15-min intervals for 2 h post-consumption (15–120 min) and later analyzed for plasma leucine, branched-chain AA (BCAA), essential AA (EAA), and total AA (TAA). Participants received a probiotic (PROB) consisting of 1 x10-9 colony forming units (CFU) Bacillus subtilis DE111 (n = 11) or a maltodextrin placebo (PL) (n = 11) for 28 days. Plasma AA response and area under the curve (AUC) values were analyzed via repeated measures analysis of variance. RESULTS: Our analysis indicated no significant (p < 0.05) differential responses for plasma leucine, BCAA, EAA, or TAA between PROB and PL from PRE to POST. AUC analysis revealed no group × time interaction for plasma leucine (p = 0.524), BCAA (p = 0.345), EAA (p = 0.512), and TAA (p = 0.712). CONCLUSION: These data indicate that 28 days of Bacillus subtilis DE111 does not affect plasma AA appearance following acute whey protein ingestion.

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.

Microbial diversity is strongly affected by the bottom-up effects of resource availability. However, because resource pools often exist as heterogeneous mixtures of distinct molecules, resource heterogeneity may also affect community diversity. To test this hypothesis, we surveyed bacterial communities in lakes that varied in resource concentration. In addition, we characterized resource heterogeneity in these lakes using an ecosystem metabolomics approach. Overall, resource concentration and resource heterogeneity affected bacterial resource-diversity relationships. We found strong relationships between bacterial alpha-diversity (richness and evenness) and resource concentration and richness, but richness and evenness responded in different ways. Likewise, we found associations between the composition of the bacterial community and both resource concentration and composition, but the relationship with resource composition was stronger. Last, in the surveyed communities the presence of resource generalists may have reduced the effect of resource heterogeneity on community composition. These results have implications for understanding the interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

Biomass burning produces black carbon (BC), effectively transferring a fraction of the biomass C from an actively cycling pool to a passive C pool, which may be stored in the soil. Yet the timescales and mechanisms for incorporation of BC into the soil profile are not well understood. The High Park fire (HPF), which occurred in northwestern Colorado in the summer of 2012, provided an opportunity to study the effects of both fire severity and geomorphology on properties of carbon (C), nitrogen (N) and BC in the Cache La Poudre River drainage. We sampled montane ponderosa pine forest floor (litter plus O-horizon) and soils at 0–5 and 5–15 cm depth 4 months post-fire in order to examine the effects of slope and burn severity on %C, C stocks, %N and BC. We used the benzene polycarboxylic acid (BPCA) method for quantifying BC. With regard to slope, we found that steeper slopes had higher C : N than shallow slopes but that there was no difference in BPCA-C content or stocks. BC content was greatest in the forest floor at burned sites (19 g BPCA-C kg−1 C), while BC stocks were greatest in the 5–15 cm subsurface soils (23 g BPCA-C m−2). At the time of sampling, unburned and burned soils had equivalent BC content, indicating none of the BC deposited on the land surface post-fire had been incorporated into either the 0–5 or 5–15 cm soil layers. The ratio of B6CA : total BPCAs, an index of the degree of aromatic C condensation, suggested that BC in the 5–15 cm soil layer may have been formed at higher temperatures or experienced selective degradation relative to the forest floor and 0–5 cm soils. Total BC soil stocks were relatively low compared to other fire-prone grassland and boreal forest systems, indicating most of the BC produced in this system is likely lost, either through erosion events, degradation or translocation to deeper soils. Future work examining mechanisms for BC losses from forest soils will be required for understanding the role BC plays in the global carbon cycle.

As glaciers thaw in response to warming, they release dissolved organic matter (DOM) to alpine lakes and streams. The United States contains an abundance of both alpine glaciers and rock glaciers. Differences in DOM composition and bioavailability between glacier types, like rock and ice glaciers, remain undefined. To assess differences in glacier and rock glacier DOM we evaluated bioavailability and molecular composition of DOM from four alpine catchments each with a glacier and a rock glacier at their headwaters. We assessed bioavailability of DOM by incubating each DOM source with a common microbial community and evaluated chemical characteristics of DOM before and after incubation using untargeted gas chromatography mass spectrometry based metabolomics (GC-MS). Prior to incubations, ice glacier and rock glacier DOM had similar C:N ratios and chemical diversity, but differences in DOM composition. Incubations with a common microbial community showed DOM from ice glacier meltwaters contained a higher proportion of bioavailable DOM (BDOM) and resulted in greater bacterial growth efficiency (BGE). After incubation, DOM composition from each source was statistically indistinguishable. This study provides an example of how MS based metabolomics can be used to assess effects of DOM composition on differences in bioavailability of DOM. Furthermore, it illustrates the importance of microbial metabolism in structuring composition of DOM. Even though rock glaciers had significantly less BDOM than ice glaciers, both glacial types still have potential to be important sources of BDOM to alpine headwaters over the coming decades.Key PointsBioavailability of organic matter released from glaciers is greater than that of rock glaciers in the Rocky Mountains.The use of GC-MS for ecosystem metabolomics represents a novel approach for examining complex organic matter pools.Both glaciers and rock glaciers supply highly bioavailable sources of organic matter to alpine headwaters in Colorado.

Lipoarabinomannan (LAM) is a lipoglycan found in abundant quantities in the cell envelope of all mycobacteria. The non-reducing arabinan termini of LAM display species-specific structural micro-heterogeneity that impacts the biological activity of the entire molecule. Mycobacterium tuberculosis, for instance, produces mannoside caps made of one to three α-(1→2)-Manp-linked residues that may be further substituted with an α-(1→4)-linked methylthio-d-xylose (MTX) residue. While the biological functions and catalytic steps leading to the formation of the mannoside caps of M. tuberculosis LAM have been well established, the biosynthetic origin and biological relevance of the MTX motif remain elusive. We here report on the discovery of a five-gene cluster dedicated to the biosynthesis of the MTX capping motif of M. tuberculosis LAM, and on the functional characterization of two glycosyltransferases, MtxS and MtxT, responsible, respectively, for the production of decaprenyl-phospho-MTX (DP-MTX) and the transfer of MTX from DP-MTX to the mannoside caps of LAM. Collectively, our NMR spectroscopic and mass spectrometric analyses of mtxS and mtxT overexpressors and knock-out mutants support a biosynthetic model wherein the conversion of 5´-methylthioadenosine, which is an ubiquitous byproduct of spermidine biosynthesis, into 5´-methylthioribose-1-phosphate precedes the formation of a 5´-methylthioribose nucleotide sugar, followed by the epimerization at C-3 of the ribose residue, and the transfer of MTX from the nucleotide sugar to decaprenyl-phosphate yielding the substrate for transfer onto LAM. The conservation of the MTX biosynthetic genes in a number of Actinomycetes suggests that this discrete glycosyl substituent may be more widespread in prokaryotes than originally thought.

As a consequence of the tight linkages among soils, plants and microbes inhabiting the rhizosphere, we hypothesized that soil nutrient and microbial stoichiometry would differ among plant species and be correlated within plant rhizospheres. We assessed plant tissue carbon (C) : nitrogen (N) : phosphorus (P) ratios for eight species representing four different plant functional groups in a semiarid grassland during near-peak biomass. Using intact plant species-specific rhizospheres, we examined soil C : N : P, microbial biomass C : N, and soil enzyme C : N : P nutrient acquisition activities. We found that few of the plant species' rhizospheres demonstrated distinct stoichiometric properties from other plant species and unvegetated soil. Plant tissue nutrient ratios and components of below-ground rhizosphere stoichiometry predominantly differed between the C4 plant species Buchloe dactyloides and the legume Astragalus laxmannii. The rhizospheres under the C4 grass B. dactyloides exhibited relatively higher microbial C and lower soil N, indicative of distinct soil organic matter (SOM) decomposition and nutrient mineralization activities. Assessing the ecological stoichiometry among plant species' rhizospheres is a high-resolution tool useful for linking plant community composition to below-ground soil microbial and nutrient characteristics. By identifying how rhizospheres differ among plant species, we can better assess how plant-microbial interactions associated with ecosystem-level processes may be influenced by plant community shifts.

Microbes cope with environmental changes by physiologically adapting to cues such as moisture and temperature. These responses happen at the molecular scale, but ultimately serve as controls on ecosystem level biogeochemical cycles. One example of this response is the accumulation of osmolytes, cellular compounds used to prevent desiccation under osmotic stress. We explored microbial biomass levels of nitrogenous osmolytes including amino acids glutamate and proline, and the tertiary amine glycine betaine, monthly in a seasonally dry California grassland using high performance liquid chromatography and either fluorescence or mass spectrometry-based detection. We also examined the behavior of amino acids in soil to analyze our ability to accurately measure putative osmolytes and determine contributions of microbial consumption and abiotic adsorption during extraction. We determined there was limited microbial consumption or abiotic adsorption of amino acids during extraction, and found no accumulation of expected nitrogenous osmolytes during the summer dry period with glutamate levels consistently 2–3% of the microbial biomass pool, and below detection limit levels of proline and glycine betaine. The lack of osmolyte use suggests the physiological response expected based on pure culture studies of individual microorganisms, and that of mixed soil consortia may be different due to a lack of sufficient osmotic stress or resource limitation in an environmental system.

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Pyrogenic carbon (PyC), the product of incomplete combustion of biomass during fire, is now recognized as a significant component of the global carbon cycle. However, quantitative determination of PyC is challenging, in particular at a large scale. We conducted a comparison of three methods for PyC analysis: benzene polycarboxylic acid (BPCA) method, hydrogen pyrolysis (hypy) and mid infrared spectroscopy (MIR) to identify a suitable approach for the determination of PyC at large geographical scales and across different environmental matrices. We analyzed samples (n = 165) derived from a variety of matrices (i.e. forest floor, soils, sediments and char), most of which were collected in the natural environment after fire. BPCA and hypy PyC estimates correlated linearly (R2 between 0.74 and 0.92), thus suggesting that they can be merged in larger scale PyC syntheses. However, the slope of the regression varied among different matrices, ranging between 0.1 and 0.44, likely due to differences in the degree of aromatic condensation. MIR coupled with partial least-squares regression (MIR-PLSR) was demonstrated to be a powerful tool for estimating PyC across a variety of environmental matrices, with high throughput and low analytical cost in comparison with the other two PyC analytical methods. Furthermore, we obtained accurate calibrations for MIR-PLSR from the hypy and the BPCA method, the latter in particular for soil samples. We thus conclude that PyC estimates at large geographical scales and across different environmental matrices can be obtained from MIR-PLSR, previous calibration with hypy or BPCA, for matrices for which the PyC yields are known.

RHM1 (1) and RHM2 (2) are highly N-methylated linear octapeptides produced by an atypical strain of Acremonium sp., cultured from a marine sponge collected in Papua New Guinea. The known peptaibiotic efrapeptin G (3) was also isolated from this fungus. The planar structures of 1 and 2 were assigned based on 1D- and 2D-NMR experiments and fragmentation patterns from ESIMS. The absolute configuration of 1 was determined via Marfey's method; the absolute configuration of 2 is proposed to be identical. Efrapeptin G (3) displayed potent cytotoxicity against murine cancer cell lines, while RHM1 (1) and RHM2 (2) showed weak cytotoxicity against murine cancer cell lines; efrapeptin G (3) and RHM1 (1) also demonstrated antibacterial activity.

cope Heat-stabilized rice bran (SRB) and cooked navy bean powder (NBP) contain a variety of phytochemicals that are fermented by colonic microbiota and may influence intestinal health. Dietary interventions with these foods should be explored for modulating colorectal cancer risk. Methods and results A randomized-controlled pilot clinical trial investigated the effects of eating SRB (30 g/day) or cooked navy bean powder (35 g/day) on gut microbiota and metabolites (NCT01929122). Twenty-nine overweight/obese volunteers with a prior history of colorectal cancer consumed a study-provided meal and snack daily for 28 days. Volunteers receiving SRB or NBP showed increased gut bacterial diversity and altered gut microbial composition at 28 days compared to baseline. Supplementation with SRB or NBP increased total dietary fiber intake similarly, yet only rice bran intake led to a decreased Firmicutes:Bacteroidetes ratio and increased SCFA (propionate and acetate) in stool after 14 days but not at 28 days. Conclusion These findings support modulation of gut microbiota and fermentation byproducts by SRB and suggest that foods with similar ability to increase dietary fiber intake may not have equal effects on gut microbiota and microbial metabolism.

The decomposition and transformation of above- and below-ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant-derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency-Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix.

Assessing the ecological importance of clouds has substantial implications for our basic understanding of ecosystems and for predicting how they will respond to a changing climate. This study was conducted in a coastal Bishop pine forest ecosystem that experiences regular cycles of stratus cloud cover and inundation in summer. Our objective was to understand how these clouds impact ecosystem metabolism by contrasting two sites along a gradient of summer stratus cover. The site that was under cloud cover ~15% more of the summer daytime hours had lower air temperatures and evaporation rates, higher soil moisture content, and received more frequent fog drip inputs than the site with less cloud cover. These cloud-driven differences in environmental conditions translated into large differences in plant and microbial activity. Pine trees at the site with greater cloud cover exhibited less water stress in summer, larger basal area growth, and greater rates of sap velocity. The difference in basal area growth between the two sites was largely due to summer growth. Microbial metabolism was highly responsive to fog drip, illustrated by an observed ~3-fold increase in microbial biomass C with increasing summer fog drip. In addition, the site with more cloud cover had greater total soil respiration and a larger fractional contribution from heterotrophic sources. We conclude that clouds are important to the ecological functioning of these coastal forests, providing summer shading and cooling that relieve pine and microbial drought stress as well as regular moisture inputs that elevate plant and microbial metabolism. These findings are important for understanding how these and other seasonally dry coastal ecosystems will respond to predicted changes in stratus cover, rainfall, and temperature.

Moisture inputs drive soil respiration (SR) dynamics in semi-arid and arid ecosystems. However, determining the contributions of root and microbial respiration to SR, and their separate temporal responses to periodic drought and water pulses, remains poorly understood. This study was conducted in a pine forest ecosystem with a Mediterranean-type climate that receives seasonally varying precipitation inputs from both rainfall (in the winter) and fog-drip (primarily in the summer). We used automated SR measurements, radiocarbon SR source partitioning, and a water addition experiment to understand how SR, and its separate root and microbial sources, respond to seasonal and episodic changes in moisture. Seasonal changes in SR were driven by surface soil water content and large changes in root respiration contributions. Superimposed on these seasonal patterns were episodic pulses of precipitation that determined the short-term SR patterns. Warm season precipitation pulses derived from fog-drip, and rainfall following extended dry periods, stimulated the largest SR responses. Microbial respiration dominated these SR responses, increasing within hours, whereas root respiration responded more slowly over days. We conclude that root and microbial respiration sources respond differently in timing and magnitude to both seasonal and episodic moisture inputs. These findings have important implications for the mechanistic representation of SR in models and the response of dry ecosystems to changes in precipitation patterns.

The structures and biological properties of peptides produced by two genera of marine-derived fungi, an atypical Acremonium sp., and a Metarrhizium sp., were explored. The Acremonium strain was isolated from a marine sponge and has previously been shown by our group to produce peptides from the efrapeptin and RHM families. The isolation and structural elucidation of the new linear pentadecapeptides efrapeptins Eα (1) and H (2) and N-methylated octapeptides RHM3 (3) and RHM4 (4) were carried out through a combination of 1D and 2D NMR techniques and tandem MS. Additional known efrapeptins E, F, and G and the known syctalidamides A and B were also isolated. The absolute configurations of 1–4 are proposed to be the same as the original compound families. The marine sponge-derived Metarrhizium sp. was shown to produce destruxin cyclic depsipeptides including A, B, B2, desmethyl B, E chlorohydrin, and E2 chlorohydrin. Efrapeptins Eα (1), F, and G each displayed IC50s of 1.3 nM against H125 cells, and destruxin E2 chlorohydrin displayed an IC50 of 160 nM against HCT-116 cells. An initial therapeutic assessment suggested a continuous (168 h) exposure of at least 2 ng/mL, or a daily (24 h) exposure of at least 300 ng/mL for H125 cells treated with efrapeptin G, and a continuous (168 h) exposure of at least 190 ng/mL for HCT-116 cells treated with destruxin E2 chlorohydrin, will cause 90% tumor cell death in vitro.

A new compound of mixed polyketide synthase-nonribosomal peptide synthetase (PKS/NRPS) origin, 11- O-methylpseurotin A ( 1), was identified from a marine-derived Aspergillus fumigatus. Bioassay-guided fractionation using a yeast halo assay with wild-type and cell cycle-related mutant strains of Saccharomyces cerevisiae resulted in the isolation of 1, which selectively inhibited a Hof1 deletion strain. Techniques including 1D and 2D NMR, HRESIMS, optical rotation, J-based analysis, and biosynthetic parallels were used in the elucidation of the planar structure and absolute configuration of 1. A related known compound, pseurotin A ( 2), was also isolated and found to be inactive in the yeast screen.

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009-13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.