The influence of aggregate size fraction and horizon position on microbial community composition

Fox, Aaron; Ikoyi, Israel; Torres-Sallan, Gemma; Lanigan, Gary; Wakelin, Steven A.; Creamer, Rachel

doi:10.1016/j.apsoil.2018.02.023

Cited by 46 publications

(37 citation statements)

References 58 publications

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“…Shifts in the microbial community composition were much less pronounced than in our previous study (22) where the overall changes in the composition of the microbiome were small though significant. This may reflect the effects of homogenization of the soils by sieving, since there is evidence that different soil fractions support distinct microbial communities (43). Communities may differ between the Ͻ2-mm fraction and the large soil aggregates (Ͼ2 mm).…”

Section: Discussionmentioning

confidence: 99%

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

Deem

Crow

et al. 2019

Appl Environ Microbiol

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The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO 2 emissions and potentially mitigates nitrous oxide emissions.Citation Yu J, Deem LM, Crow SE, Deenik J, Penton CR. 2019. Comparative metagenomics reveals enhanced nutrient cycling potential after 2 years of biochar amendment in a tropical oxisol. Appl Environ Microbiol 85:e02957-18. https://doi.

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Section: Discussionmentioning

confidence: 99%

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

Deem

Crow

et al. 2019

Appl Environ Microbiol

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“…The interrelationships of environmental parameters among taxonomic subgroups may play a regulating role [20]. Beta diversity results of PCoA and PERMANOVA also showed that N30 had no significant effect on the community composition of bacteria and fungi; however, bacteria displayed a significant difference at N90, while the difference became evident for fungi at N60.…”

Section: Microbial Community Composition and Structurementioning

confidence: 93%

“…Changes induced by SND in microhabitats involve a series of tortuous physical networks, which determine the flow of substrates and solutes over space and time, influencing microbial interactions [20]. The decrease in soil pH caused by N deposition is one of the main factors affecting the change in soil microbial composition and functional diversity [6].…”

Section: Main Characteristics Of Microhabitat-microbial Interactions mentioning

confidence: 99%

“…Soil microorganisms can be affected by N deposition and features of the soil microhabitat, such as pH [13][14][15], bulk density and water-holding capacity [16,17], particulate size [18,19], and aggregate stability [20,21]. However, alterations in the composition of soil microbial communities due to changes in pH and particle size as a result of N deposition are not well understood despite the importance of microbial communities in the N cycle [15,22,23].…”

Section: Introductionmentioning

confidence: 99%

“…Particle-size fractionation, which allows the separation of soil organic matter with varying degrees of microbial alteration, might help elucidate microbe-mediated soil carbon (C) and N cycling characteristics [28,29]. Microbial acquisition of a substrate is compounded by relatively stable C and N levels [30], high nutrient and O 2 availability [31], and adsorption of extracellular enzymes to the clay and silt fractions but not to their aggregates [20]. As soil changes induced by N deposition are mainly the result of microbiological processes, different substrates and soil properties are selected by specifically adapted microbial communities [18,29].…”

Section: Introductionmentioning

confidence: 99%

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Variations in the Compositions of Soil Bacterial and Fungal Communities Due to Microhabitat Effects Induced by Simulated Nitrogen Deposition of a Bamboo Forest in Wetland

Huang²,

Ekawati

et al. 2019

Forests

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Although numerous studies have been published on nitrogen (N) deposition, little is known about its impact on microbial communities in wetland forests. Here, we used simulated nitrogen deposition (SND) to analyze the importance of differences in soil microhabitats in promoting the diversity of soil bacteria and fungi. We compared various levels of SND (control (CK), low N (N30), medium N (N60), and high N (N90)) and found that these were associated with changes in soil microhabitats. Additionally, SND affected soil pH, clay and sand content of the soil, and specific surface area (SSA). Bacteria and fungi responded differently to increased SND levels. The alpha diversity of bacteria decreased with an increased SND level, while fungal abundance, diversity, and community evenness reached their maximum values at the N60 threshold. Principal coordinates analysis (PCoA), nonparametric multivariate analysis of variance (PERMANOVA), and linear discriminant analysis (LDA) coupled with effect size measurements (LefSe) also confirmed that the bacterial composition was different at N90 compared to other levels of SND while that of fungi was different at N60. A higher discriminant level (LDA score ≥4) may be a valuable index of selecting indicator microbial clades sensitive to SND for wetland management. Further, an increased pH was associated with a greater abundance of bacteria and fungi. In addition, the volume contents of clay and SSA were negatively correlated with bacteria but fungi are associated with soil specific gravity (SSG). Overall, in a neutral soil pH environment, pH fluctuation is the main influencing factor in terms of bacterial and fungal abundance and diversity. The diversity of fungi is more dependent on the type and relative content of solid phase components in soil than that of bacteria, implying the presence of species-specific niches for bacteria and fungi. These results demonstrate that changes in SND can induce short-term microbial and microhabitat changes.

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Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

Amelung,

Tang,

Siebers

et al. 2023

J. Plant Nutr. Soil Sci.

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The functions of soils are intimately linked to their three‐dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi‐isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting‐edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates.

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The influence of aggregate size fraction and horizon position on microbial community composition

Cited by 46 publications

References 58 publications

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

Variations in the Compositions of Soil Bacterial and Fungal Communities Due to Microhabitat Effects Induced by Simulated Nitrogen Deposition of a Bamboo Forest in Wetland

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

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