The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of ...PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.
Wetlands have numerous critical ecological functions, some of which are regulated by several nitrogen (N) and carbon (C) biogeochemical processes, such as denitrification, organic matter ...decomposition, and methane emission. Until now, the underlying pathways of the effects of environmental and biological factors on wetland N and C cycling rates are still not fully understood. Here, we investigated soil potential/net nitrification, potential/unamended denitrification, methane production/oxidation rates in 36 riverine, lacustrine, and palustrine wetland sites on the Tibet Plateau. The results showed that all the measured N and C cycling rates did not differ significantly among the wetland types. Stepwise multiple regression analyses revealed that soil physicochemical properties (e.g., moisture, C and N concentration) explained a large amount of the variance in most of the N and C cycling rates. Microbial abundance and diversity were also important in controlling potential and unamended denitrification rates, respectively. Path analysis further revealed that soil moisture and N and C availability could impact wetland C and N processes both directly and indirectly. For instance, the indirect effect of soil moisture on methane production rates was mainly through the regulating the soil C content and methanogenic community structure. Our findings highlight that many N and C cycling processes in high-altitude and remote Tibetan wetlands are jointly regulated by soil environments and functional microorganisms. Soil properties affecting the N and C cycling rates in wetlands through altering their microbial diversity and abundance represent an important but previously underestimated indirect pathway.
Identification of nanoplastics in complex environmental matrices remains a challenge. Despite the increase in nanoplastics studies, there is a lack of studies dedicated to nanoplastics detection, ...partially explained by their carbon-based structure, their wide variety of composition, and their low environmental concentrations compared to the natural organic matter. Here, pyrolysis coupled to a GCMS instrumental setup provided a relevant analytical response for polypropylene and polystyrene nanoplastic suspensions. Specific pyrolysis markers and their indicative fragment ions were selected and validated. Possible interferences with environmental matrices were explored by spiking nanoplastics in various organic matter suspensions (i.e., algae, soil natural organic matter, and soil humic acid) and analyzing an environmental suspension of nanoplastics. While a rapid polypropylene nanoplastics identification was validated, polystyrene nanoplastics require preliminary treatment. The strategies presented herein open new possibilities for the detection/identification of nanoplastics in environmental matrices such as soil, dust, and biota.
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•Ball-milled and < 2 mm soils showed similar accuracy in MIR and NIR spectral models.•Grinding soils did not improve the accuracy in both MIR and NIR models.•MIR/NIR spectroscopy can ...distinguish first horizon from subsurface horizon soils.•Chemical information is the same in ball-milled and < 2 mm spectra models.•MIR/NIR spectroscopy can be used to determine a range of soil attributes.
This study evaluated the influence on predicted physical and chemical parameters of soil particle sizes commonly used in the infrared spectra acquisition, < 0.100 mm (ball-milled) and < 2 mm for MIR and NIR ranges, respectively. The influences were evaluated through the accuracy (RMSEP and RPIQ) results and the chemical information extracted by multivariate classification and regression models. For this a national population of soils containing 888 samples from 225 modal soil profiles, each with the reference values of sand, silt, clay, pH(CaCl2), pH(Water), total carbon, organic carbon (OC), cation exchange capacity, nitrogen, aluminium and bulk density, was used. Spectra were collected in MIR and NIR ranges using samples with both particle sizes. For each soil attribute, 29 random calibration and validation sets were generated and SVM, PLS and Cubist regression models were built. This same strategy was used to classify the soil samples according to their respective horizons (1 or 2-7) using SVM, PLS-DA and random forest algorithms. Results obtained by the randomised calibration and validation set did not present positive or negative bias on the RMSEP and RPIQ values based on soil particle sizes. In general, random variations of the RMSEP and RPIQ values were observed for all soil attributes. In addition, ball-milled and < 2 mm spectral models did not present large differences in both accuracy parameters simultaneously. The median Matthews correlation coefficient values calculated by the classification models showed minor variations of 2.61% and 0.65% for samples from both particle sizes in MIR and NIR ranges, respectively. The ‘Variable Importance in Projection’ or VIP scores, calculated by PLS and PLS-DA models, did not show any large variation in the chemical information extracted from MIR and NIR spectra for models built using samples from both particle sizes. The results from this study show that scanning ball-milled or < 2 mm sieved soil samples will result in spectra models in MIR and NIR ranges with the same accuracy and same chemical information. This suggests there is a big potential to eliminate the ball-milling sample step in soil laboratories that use MIR and NIR vibrational spectroscopy techniques to predict soil attributes, thereby reducing the time and costs associated with soil analysis.
Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment ...settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.
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•A compact, robust, and field-capable device based on LIBS principle was developed.•LIBS was employed to estimate total soil carbon content in mineral soil samples.•LIBS results were ...validated using LECO measurements on the same samples.•Spatial mapping of carbon content in soil (1–85 g·kg−1) has been performed.•Calibration model was found robust in utilization to fresh samples from various fields.
Soil carbon storage is a substantial factor in the global carbon cycle. Carbon sequestration in agricultural soils, and the assessment and validation of soil carbon storage, are crucial for the mitigation of agricultural greenhouse gas emissions and for steering towards sustainable farming practices. Enforcement and verification of carbon sequestration policies, methods, and models require extensive soil carbon monitoring capability. However, current conventional laboratory-based methods for soil carbon estimation are laborious, expensive, and time-consuming. In this work, we have developed a compact, robust, and field-capable experimental device based on laser-induced breakdown spectroscopy (LIBS) for the rapid assessment of total soil carbon content and its spatial distribution in mineral soils. The carbon content quantification was performed using a spectral line of carbon at a wavelength of 193.1 nm emitted from the laser-induced plasma plume. The LIBS measurements were performed on soil samples collected from 28 different locations and various depths (up to 1 m) of a test field cultivated with a forage legume (red clover - Trifolium pratense, L.) and grass (Timothy - Phleum pratense, L.) mixture in eastern Finland. A calibration model was established based on a limited and randomly chosen sample set and validated by comparing soil carbon estimates obtained from various locations in the test field using the dry combustion (LECO) method. Further, we demonstrate here the usefulness of LIBS methodology for mapping three-dimensional carbon distribution at the test field. We emphasize here that the calibration model can be generalized to other sample areas under similar soil type with a relative error of less than 10 % and possesses potential for fast on-site determination of spatial variation in total soil carbon, reducing substantially the need of time-consuming sample processing in laboratory. Therefore, LIBS enables frequent and extensive spatial and temporal soil carbon mapping and has the potential to become part of the future carbon monitoring network.
There are a variety of complementary observations that could be used in the search for life in extraterrestrial settings. At the molecular scale, patterns in the distribution of organics could ...provide powerful evidence of a biotic component. In order to observe these molecular biosignatures during spaceflight missions, it is necessary to perform separation science in situ. Microchip electrophoresis (ME) is ideally suited for this task. Although this technique is readily miniaturized and numerous instruments have been developed over the last 3 decades, to date, all lack the automation capabilities needed for future missions of exploration. We have developed a portable, automated, battery-powered, and remotely operated ME instrument coupled to laser-induced fluorescence detection. This system contains all the necessary hardware and software interfaces for end-to-end functionality. Here, we report the first application of the system for amino acid analysis coupled to an extraction unit in order to demonstrate automated sample-to-data operation. The system was remotely operated aboard a rover during a simulated Mars mission in the Atacama Desert, Chile. This is the first demonstration of a fully automated ME analysis of soil samples relevant to planetary exploration. This validation is a critical milestone in the advancement of this technology for future implementation on a spaceflight mission.
The use of rock dust in agriculture has increased worldwide and particularly in Brazil since its regulation by Law 12.890 (2013). However, some inconsistent results in standard chemical analysis of ...soils amended with rock dust have drawn attention, and among them, cation exchange capacity (CEC). This paper evaluates the increase in sum of bases (SB) and CEC of two soils amended with commercial rock dust (magnesium silicate), measured by four methods: ion exchange resin, potassium chloride (KCl), compulsive exchange and cesium adsorption. The maximum possible increase of SB in the soil was estimated based on the total chemical analysis of the rock dust and compared to the measured CEC results. We concluded the resin method inflated the results, due to the dissolution of rock dust particles by the acid extraction used to recover the adsorbed cations in resin beads. These extra cations caused overestimation of the sum of bases and consequently, of the estimated CEC. Among the methods used, direct CEC methods were more appropriate, as well as the KCl, since it does not employ acid extractions at any step. In addition, calculations based on the total chemical analysis of the rock dust can help to identify some of the cases in which the routine analysis is inflated by the dissolution of rock dust.
The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas ...oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.
The stability of biochar carbon (C) is the major determinant of its value for long-term C sequestration in soil. A long-term (5 year) laboratory experiment was conducted under controlled conditions ...using 11 biochars made from five C3 biomass feedstocks (Eucalyptus saligna wood and leaves, papermill sludge, poultry litter, cow manure) at 400 and/or 550 °C. The biochars were incubated in a vertisol containing organic C from a predominantly C4-vegetation source, and total CO2–C and associated δ13C were periodically measured. Between 0.5% and 8.9% of the biochar C was mineralized over 5 years. The C in manure-based biochars mineralized faster than that in plant-based biochars, and C in 400 °C biochars mineralized faster than that in corresponding 550 °C biochars. The estimated mean residence time (MRT) of C in biochars varied between 90 and 1600 years. These are conservative estimates because they represent MRT of relatively labile and intermediate-stability biochar C components. Furthermore, biochar C MRT is likely to be higher under field conditions of lower moisture, lower temperatures or nutrient availability constraints. Strong relationships of biochar C stability with the initial proportion of nonaromatic C and degree of aromatic C condensation in biochar support the use of these properties to predict biochar C stability in soil.
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