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Soil microbial traits and functions play a central role in soil organic carbon (SOC) dynamics. However, at the macroscale (regional to global) it is still unresolved whether (i) specific environmental attributes (e.g., climate, geology, soil types) or (ii) microbial community composition drive key microbial traits and functions directly. To address this knowledge gap, we used 33 grassland topsoils (0-10 cm) from a geoclimatic gradient in Chile. First, we incubated the soils for 1 week in favorable standardized conditions and quantified a wide range of soil microbial traits and functions such as microbial biomass carbon (MBC), enzyme kinetics, microbial respiration, growth rates as well as carbon use efficiency (CUE). Second, we characterized climatic and physicochemical properties as well as bacterial and fungal community composition of the soils. We then applied regression analysis to investigate how strongly the measured microbial traits and functions were linked with the environmental setting versus microbial community composition. We show that environmental attributes (predominantly the amount of soil organic matter) determined patterns of MBC along the gradient, which in turn explained microbial respiration and growth rates. However, respiration and growth normalized for MBC (i.e., specific respiration and growth) were more linked to microbial community composition than environmental attributes. Notably, both specific respiration and growth followed distinct trends and were related to different parts of the microbial community, which in turn resulted in strong effects on microbial CUE. We conclude that even at the macroscale, CUE is the result of physiologically decoupled aspects of microbial metabolism, which in turn is partially determined by microbial community composition. The environmental setting and microbial community composition affect different microbial traits and functions, and therefore both factors need to be considered in the context of macroscale SOC dynamics.

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BACKGROUND: Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove. RESULTS: Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified. CONCLUSION: The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

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The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.

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Soil enzymes play a fundamental role in nutrient cycling in forest systems. The stoichiometry of C, N, and P­acquiring enzymes has been used to indicate nutrient limitation in the soil. However, the enzymatic stoichiometry remains poorly understood in pure and mixed eucalypt plantations. Thus, this study aims to assess the activity of enzymes in the soil to address the hypothesis that the introduction of N2-fixing trees could influence the enzymatic stoichiometry on C, N, and P cycling. The activity of ß-glucosidase (BG), urease (U), and acid phosphatase (AP) was assessed in soil (0-20 cm depth) of pure Eucalyptus grandis without (E) and with N fertilization (E+N), and a mixed system with E. grandis and Acacia mangium (E+A), and a pure A. mangium (A) plantation at 27 and 39 months after planting. The activities of BG/U, BG/AP, and U/AP were used to calculate the enzyme C/N, C/P, and N/P ratios, respectively. Rates of N­acquiring enzymes were higher in E and E+N, while soil microorganisms invested in P­acquiring enzymes in A and E+A. The vector length and angle demonstrated that C demand by microorganisms does not change in relation to N and P, regardless of the treatment. However, N demand decreased in relation to P in A and E+A (mainly at 27 months). Our results suggest that enzymes activity in pure eucalypt systems is limited for their soil-litter nutrient contents. At the same time while acacia and mixed plantation seem to invest in P­acquiring enzymes to improve biological N2 fixation promoted by diazotrophic bacteria associated to acacia.

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Leishmania are sandfly-transmitted protists that induce granulomatous lesions in their mammalian host. Although infected host cells in these tissues can exist in different activation states, the extent to which intracellular parasites stages also exist in different growth or physiological states remains poorly defined. Here, we have mapped the spatial distribution of metabolically quiescent and active subpopulations of Leishmania mexicana in dermal granulomas in susceptible BALB/c mice, using in vivo heavy water labeling and ultra high-resolution imaging mass spectrometry. Quantitation of the rate of turnover of parasite and host-specific lipids at high spatial resolution, suggested that the granuloma core comprised mixed populations of metabolically active and quiescent parasites. Unexpectedly, a significant population of metabolically quiescent parasites was also identified in the surrounding collagen-rich, dermal mesothelium. Mesothelium-like tissues harboring quiescent parasites progressively replaced macrophage-rich granuloma tissues following treatment with the first-line drug, miltefosine. In contrast to the granulomatous tissue, neither the mesothelium nor newly deposited tissue sequestered miltefosine. These studies suggest that the presence of quiescent parasites in acute granulomatous tissues, together with the lack of miltefosine accumulation in cured lesion tissue, may contribute to drug failure and nonsterile cure.IMPORTANCE Many microbial pathogens switch between different growth and physiological states in vivo in order to adapt to local nutrient levels and host microbicidal responses. Heterogeneity in microbial growth and metabolism may also contribute to nongenetic mechanisms of drug resistance and drug failure. In this study, we have developed a new approach for measuring spatial heterogeneity in microbial metabolism in vivo using a combination of heavy water (2H2O) labeling and imaging mass spectrometry. Using this approach, we show that lesions contain a patchwork of metabolically distinct parasite populations, while the underlying dermal tissues contain a large population of metabolically quiescent parasites. Quiescent parasites also dominate drug-depleted tissues in healed animals, providing an explanation for failure of some first line drugs to completely eradicate parasites. This approach is broadly applicable to study the metabolic and growth dynamics in other host-pathogen interactions.

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In east-central Brazil, the Ediacaran-Cambrian Bambuí Basin has the potential to provide a record of unique geochemical responses of Earth's ocean and atmosphere evolution during this key time interval. From this perspective, we studied an interval of the upper Bambuí Basin using sedimentologic, stratigraphic, and chemostratigraphic tools. The lower Cambrian Jaíba Member of the uppermost Serra da Saudade Formation is an interval of up to 60 m-thick of carbonate rocks disposed into two shallowing upward trends. Inner to outer ramp and high-energy shoal deposits are described, in which laminated microbialites are the prevailing sedimentary facies. REE + Y data suggest contamination by iron (oxy)hydroxides that are dissociated from the riverine detritic flux. Sedimentary iron enrichment may be related to the settling of iron nanoparticles in coastal environments, diagenetic iron mobilization, or both. MREE enrichment is caused by microbial degradation of organic matter in the iron reduction zone during the anoxic early-diagenetic stage. Chromium isotopes yielded negatively fractionated values (δ53 Cr = -0.69 to -0.27‰), probably resulting from biotic and abiotic reduction of dissolved Cr(VI) to light and less toxic Cr(III) within pores of microbial mats. The δ53 Cr data of the Jaíba microbialite are thus a product of metabolic reactions in microbial mats and do not reflect seawater signal. The isotopic offset from seawater is feasible from molecular diffusion of Cr into pore water and reduction reactions occurring deep inside the mat, although the exact mechanism and consequences are not yet fully understood due to the poor preservation of metabolic reactions in the geological record. Our study suggests that Cr isotopes can be used to reconstruct Cr and other metals cycling within ancient microbial mats, and that caution should be taken when using past microbialites to infer seawater Cr records and redox state of the atmosphere and ocean.

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The highland forests of tropical regions are highly vulnerable to climate change because changes in soil organic quality due to the increased soil water deficit conditions through rising temperatures. Several authors have reported that labile molecules dominate soil organic matter at higher elevations, and it is therefore more vulnerable to the rising temperatures associated with climate change. The objective of the present study was to analyze the effect of interaction between the chemical composition of organic matter derived from the dominant plant species and the metabolism of microbial community along an elevational gradient in a highland forest in Central Mexico. The study compared three vegetation-soil systems that represent three different elevational levels: Alnus-system (3100 m.a.s.l.), Abies-system (3500 m.a.s.l.) and Pinus-system (3700 m.a.s.l.). The SOM produced in the lowest site is more recalcitrant (i.e., higher Alkyl:O-Alkyl ratio) as a result of the lower water availability than in the highest site. The results of Threshold Elemental RatioC:N (TERC:N) and TERC:P for the organic layer were lower than their C:N and C:P ratios in the organic layer, supporting that the microbial community of the organic layer in the site of lowest elevation must be limited by the carbon source, rather than by N and P. However, these results were not found in the mineral soil, suggesting that the drivers of organic matter decomposition differ between the organic layer and the mineral soil. As a conclusion, our results suggest that the chemical recalcitrance of organic matter (at the lowest site) and temperature (at the highest site) reduce the microbial metabolic activity in the forest floor. Integrated study of plant-derived organic material and the microbial metabolism of the forest floor is therefore required to achieve a full understanding of the vulnerability of tropical mountain ecosystems to climate change.

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We studied petroleum biodegradation by biostimulation by using water in oil in water (W/O/W) double emulsions. These emulsions were developed using seawater, canola oil, surfactants, and mineral salts as sources of NPK. The emulsions were used in the simulation of hydrocarbon bioremediation in oligotrophic sea water. Hydrocarbon biodegradation was evaluated by CO2 emissions from microcosms. We also evaluated the release of inorganic nutrients and the stability of the emulsion's droplets. The double emulsions improved CO2 emission from the microcosms, suggesting the increase in the hydrocarbon biodegradation. Mineral nutrients were gradually released from the emulsions supporting the hydrocarbon biodegradation. This was attributed to the formation of different diameters of droplets and therefore, varying stabilities of the droplets. Addition of the selected hydrocarbonoclastic isolates simulating bioaugmentation improved the hydrocarbon biodegradation. We conclude that the nutrient-rich W/O/W emulsion developed in this study is an effective biostimulation agent for bioremediation in oligotrophic aquatic environments.

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L-Asparaginase amidohydrolase (EC 3.5.1.1) has received significant attention owing to its clinical use in acute lymphoblastic leukemia treatment and non-clinical applications in the food industry to reduce acrylamide (toxic compound) formation during the frying of starchy foods. In this study, a sequential optimization strategy was used to determine the best culture conditions for L-asparaginase production from filamentous fungus Aspergillus terreus CCT 7693 by submerged fermentation. The cultural conditions were studied using a 3-level, central composite design of response surface methodology, and biomass and enzyme production were optimized separately. The highest amount of biomass (22.0 g·L-1) was obtained with modified Czapek-Dox medium containing glucose (14 g·L-1), L-proline (10 g·L-1), and ammonium nitrate (2 g·L-1) fermented at 37.2 °C and pH 8.56; for maximum enzyme production (13.50 U·g-1), the best condition was modified Czapek-Dox medium containing glucose (2 g·L-1), L-proline (10 g·L-1), and inoculum concentration of 4.8 × 108 espore·mL-1 adjusted to pH 9.49 at 34.6 °C. The L-asparaginase production profile was studied in a 7 L bench-scale bioreactor and a final specific activity of 13.81 U·g-1 was achieved, which represents an increase of 200% in relation to the initial non-optimized conditions.

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Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia.

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