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Organic Matter and Mineral Composition of Silicate Soils: FTIR Comparison Study by Photoacoustic, Diffuse Reflectance, and Attenuated Total Reflection Modalities
This study aims to compare photoacoustic (FTIR–PAS), diffuse reflectance (DRIFT), and attenuated total reflection (ATR) FTIR modalities in the wide wavenumber range from NIR (7500 cm−1) to FIR (150 cm−1) for the same silicate soil samples under the same conditions. The possibilities of non-destructive rapid qualitative analysis of soils by these modalities without comprehensive data treatment were compared. The assignment of more than 100 bands for the chernozem and sod-podzolic as common types of silicate types of soil was made. The following groups of bands of organic matter and inorganic matrix were reliably found in spectra of all or at least two modalities: 3690–3680 cm−1 (hydrogen-bonded SiO–H…H2O stretch, not ATR), 2930–2910 cm−1 and 2860–2850 cm−1 (methylene stretch), 1390–1380 cm−1, (symmetric stretch carboxylate, DRIFT and FTIR–PAS); 2000–1990 cm−1, 1885 cm−1, and 1790–1783 cm−1 (SiO2 overtones, DRIFT and FTIR–PAS), 1163–1153 cm−1, SiO2 lattice (not FTIR–PAS), 1037 cm−1 (Si–O or Al–O stretch), 796 cm−1 (lattice symmetrical Si–O–Si stretch); 697 cm−1, SiO2; and 256 cm−1 (not FTIR–PAS). Amide I, II, and III bands appear in DRIFT and FTIR–PAS spectra while not in ATR. Except for methylene and carboxylate groups, CH vibrations (3100–2900 cm−1) are not seen in ATR. Bands at 1640–1630 cm−1, 1620–1610 cm−1, 1600–1598 cm−1 (primary water bands and probably carboxylate) appear in the spectra of all three modalities but are unresolved and require data treatment. It is preferable to use all three modalities to characterize both soil organic matter and mineral composition. DRIFT provides the maximum number of bands in all three modalities and should be selected as a primary technique in the NIR and 4000–2000 cm−1 regions for hydrogen-bonding bands, CHX groups, and the silicate matrix. ATR–FTIR complements DRIFT and provides a good sensitivity for soil water and the matrix in 2000–400 cm−1. FTIR–PAS in 4000–1500 cm−1 reveals more bands than DRIFT and shows the highest sensitivity for absorption bands that do not appear in DRIFT or ATR-IR spectra. Thus, FTIR–PAS is expedient for supporting either DRIFT or ATR–FTIR. This modality comparison can be a basis for methodological support of IR spectroscopy of soils and similar organomineral complexes.
Journal Article
Up in the garden and down in the dirt
\"Up in the garden, the world is full of green--leaves and sprouts, growing vegetables, ripening fruit. But down in the dirt there is a busy world of earthworms digging, snakes hunting, skunks burrowing, and all the other animals that make a garden their home. In this exuberant book, discover the wonder and activity that lie hidden between the stalks, under the shade of leaves ... and down in the dirt.\"-- Provided by publisher.
Book
Soil biodiversity and soil community composition determine ecosystem multifunctionality
Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth’s biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.
Journal Article
Soil microbial communities are shaped by plant-driven changes in resource availability during secondary succession
Although we understand the ecological processes eliciting changes in plant community composition during secondary succession, we do not understand whether co-occurring changes in plant detritus shape saprotrophic microbial communities in soil. In this study, we investigated soil microbial composition and function across an old-field chronosequence ranging from 16 to 86 years following agricultural abandonment, as well as three forests representing potential late-successional ecosystems. Fungal and bacterial community composition was quantified from ribosomal DNA, and insight into the functional potential of the microbial community to decay plant litter was gained from shotgun metagenomics and extracellular enzyme assays. Accumulation of soil organic matter across the chronosequence exerted a positive and significant effect on fungal phylogenetic β-diversity and the activity of extracellular enzymes with lignocellulolytic activity. In addition, the increasing abundance of lignin-rich C
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grasses was positively related to the composition of fungal genes with lignocellulolytic function, thereby linking plant community composition, litter biochemistry, and microbial community function. However, edaphic properties were the primary agent shaping bacterial communities, as bacterial β-diversity and variation in functional gene composition displayed a significant and positive relationship to soil pH across the chronosequence. The late-successional forests were compositionally distinct from the oldest old fields, indicating that substantial changes occur in soil microbial communities as old fields give way to forests. Taken together, our observations demonstrate that plants govern the turnover of soil fungal communities and functional characteristics during secondary succession, due to the continual input of detritus and differences in litter biochemistry among plant species.
Journal Article
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
Journal Article
Endemism and functional convergence across the North American soil mycobiome
Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure–function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.
Journal Article
Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes‐to‐Amazon elevation gradient
The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil‐derived CO₂ released to the atmosphere. We studied tropical lowland, premontane and montane forest soils taken from along a 3200‐m elevation gradient located in south‐east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C‐cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram‐positive relative to gram‐negative bacteria explaining much of the model variance. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes.
Journal Article
Plant litter chemistry and microbial priming regulate the accrual, composition and stability of soil carbon in invaded ecosystems
Soil carbon (C) sequestration, as an ecosystem property, may be strongly influenced by invasive plants capable of depositing disproportionately high quantities of chemically distinct litter that disrupt ecosystem processes. However, a mechanistic understanding of the processes that regulate soil C storage in invaded ecosystems remains surprisingly elusive. Here, we studied the impact of the invasion of two noxious nonnative species, Polygonum cuspidatum, which produces recalcitrant litter, and Pueraria lobata, which produces labile litter, on the quantity, molecular composition, and stability of C in the soils they invade. Compared with an adjacent noninvaded old‐field, P. cuspidatum‐invaded soils exhibited a 26% increase in C, partially through selective preservation of plant polymers. Despite receiving a 22% higher litter input, P. lobata‐invaded Pinus stands exhibited a 28% decrease in soil C and a twofold decrease in plant biomarkers, indicating microbial priming of native soil C. The stability of C exhibited an opposite trend: the proportion of C that was resistant to oxidation was 21% lower in P. cuspidatum‐invaded soils and 50% higher in P. lobata‐invaded soils. Our results highlight the capacity of invasive plants to feed back to climate change by destabilizing native soil C stocks and indicate that environments that promote the biochemical decomposition of plant litter would enhance the long‐term storage of soil C. Further, our study highlights the concurrent influence of dominant plant species on both selective preservation and humification of soil organic matter.
Journal Article
Biochar adsorbed ammonia is bioavailable
Biochar is produced as a by-product of the low temperature pyrolysis of biomass during bioenergy extraction and its incorporation into soil is of global interest as a potential carbon sequestration tool. Biochar influences soil nitrogen transformations and its capacity to take up ammonia is well recognized. Anthropogenic emissions of ammonia need to be mitigated due to negative environmental impacts and economic losses. Here we use an isotope of nitrogen to show that ammonia-N adsorbed by biochar is stable in ambient air, but readily bioavailable when placed in the soil. When biochars, containing adsorbed 15N labelled ammonia, were incorporated into soil the 15N recovery by roots averaged 6.8% but ranged from 26.1% to 10.9% in leaf tissue due to differing biochar properties with plant 15N recovery greater when acidic biochars were used to capture ammonia. Recovery of 15N as total soil nitrogen (organic+inorganic) ranged from 45% to 29% of 15N applied. We provide a proof of concept for a synergistic mitigation option where anthropogenic ammonia emissions could be captured using biochar, and made bioavailable in soils, thus leading to nitrogen capture by crops, while simultaneously sequestering carbon in soils.
Journal Article