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"Soil ecology"
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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
The Ecology of Soil Carbon: Pools, Vulnerabilities, and Biotic and Abiotic Controls
Soil organic matter (SOM) anchors global terrestrial productivity and food and fiber supply. SOM retains water and soil nutrients and stores more global carbon than do plants and the atmosphere combined. SOM is also decomposed by microbes, returning CO
2
, a greenhouse gas, to the atmosphere. Unfortunately, soil carbon stocks have been widely lost or degraded through land use changes and unsustainable forest and agricultural practices.
To understand its structure and function and to maintain and restore SOM, we need a better appreciation of soil organic carbon (SOC) saturation capacity and the retention of above- and belowground inputs in SOM. Our analysis suggests root inputs are approximately five times more likely than an equivalent mass of aboveground litter to be stabilized as SOM. Microbes, particularly fungi and bacteria, and soil faunal food webs strongly influence SOM decomposition at shallower depths, whereas mineral associations drive stabilization at depths greater than ∼30 cm. Global uncertainties in the amounts and locations of SOM include the extent of wetland, peatland, and permafrost systems and factors that constrain soil depths, such as shallow bedrock. In consideration of these uncertainties, we estimate global SOC stocks at depths of 2 and 3 m to be between 2,270 and 2,770 Pg, respectively, but could be as much as 700 Pg smaller. Sedimentary deposits deeper than 3 m likely contain >500 Pg of additional SOC. Soils hold the largest biogeochemically active terrestrial carbon pool on Earth and are critical for stabilizing atmospheric CO
2
concentrations. Nonetheless, global pressures on soils continue from changes in land management, including the need for increasing bioenergy and food production.
Journal Article
Dirt
Brief text explores how soil is formed, its layers, and its importance as a natural resource that living things need to survive.
Book
Soil biodiversity and soil erosion: It is time to get married: Adding an earthworm factor to soil erosion modelling
Aim: The relationship between erosion and biodiversity is reciprocal. Soil organisms can both reduce soil loss, by improving porosity, and increase it, by diminishing soil stability as a result of their mixing activities. Simultaneously, soil runoff has ecological impacts on belowground communities. Despite clear research into interactions, soil erosion models do not consider biodiversity in their estimates and soil ecology has poorly investigated the effects of erosion. In order to start filling in these research gaps, we present a novel biological factor and introduce it into a well-known soil erosion model (the revised universal soil loss equation). Furthermore, we propose insights to advance soil erosion ecology. Location: Pan-European. Time period: Simulation of present-day conditions. Major taxa studied: Earthworms. Methods: We present three pathways to fill in current knowledge gaps in soil biodiversity and erosion studies: (a) introducing a biological factor into soil erosion models; (b) developing plot-scale experiments to clarify and quantify the positive/negative effects of soil organisms on erosion; (c) promoting ecological studies to assess both short- and long-term effects of soil erosion on soil biota. Results: We develop a biological factor to be included in soil erosion modelling. Thanks to available data on earthworm diversity (richness and abundance), we generate an \"earthworm factor\", incorporate it into a model of soil erosion and produce the first pan-European maps of it. Main conclusions: New estimates of soil loss can be generated by including biological factors in soil erosion models. At the same time, the effects of soil loss on below-ground diversity require further investigation. Available data and technologies make both processes possible. We think that it is time to commit to fostering the fundamental, although complex, relationship between soil biodiversity and erosion.
Journal Article
Dirt
Brief text explores how soil is formed, its layers, and its importance as a natural resource that living things need to survive.
Book
Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function
ABSTRACT
Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.
The microbial perspective, including microscale microbial interactions, is a crucial component of the soil environment that must be considered when measuring soil processes and developing predictive ecosystem models.
Journal Article
A world without soil : the past, present, and precarious future of the Earth beneath our feet
A scientist's manifesto addressing a soil loss crisis accelerated by poor conservation practices and climate change.
Book
Soil nematode abundance and functional group composition at a global scale
Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 10
20
nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios.
High-resolution spatial maps of the global abundance of soil nematodes and the composition of functional groups show that soil nematodes are found in higher abundances in sub-Arctic regions, than in temperate or tropical regions.
Journal Article