Journal: Soil Biology and Biochemistry

Abbreviation

Soil biol. biochem.

Publisher

Elsevier

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ISSN

0038-0717
1879-3428

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Publications1 - 10 of 123
  • Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features
    Item type: Journal Article
    Burns, Kayla N.; Kluepfel, Daniel A.; Strauss, Sarah L.; et al. (2015)
    Soil Biology and Biochemistry
    Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.
  • Dark septate hyphomycetes in Swiss conifer forest soils surveyed using Norway spruce seedlings as bait
    Item type: Journal Article
    Ahlich, K.; Rigling, D.; Holdenrieder, O.; et al. (1998)
    Soil Biology and Biochemistry
  • Denitrification in grass swards is increased under elevated atmospheric CO2
    Item type: Journal Article
    Baggs, E.M.; Richter, M.; Cadisch, Georg; et al. (2003)
    Soil Biology and Biochemistry
  • Decadal nutrient addition reveals phosphorus limitation and its adaptive mechanisms in tropical rainforests
    Item type: Journal Article
    Yu , Qingshui; Anthony, Mark A.; Gessler, Arthur; et al. (2025)
    Soil Biology and Biochemistry
    Tropical rainforests on low-phosphorus soils are highly biodiverse and productive, playing a crucial role in climate change mitigation. However, the degree of phosphorus limitation and potential adaptation mechanisms of tropical rainforests remain unclear. Here, we conducted a decade-long field experiment with nitrogen (N) and phosphorus (P) additions in primary and secondary tropical rainforests. We investigated growth responses of 2012 individual trees and explored how litter, soil, and microbes contribute to maintaining P availability for plants. We found that the P addition alone enhanced tree growth in both rainforests. Adding P (alone or with N) increased the average leaf P concentrations of eight species but reduced P resorption efficiency (PRE), soil phosphatase activity, and fungal diversity in the two forests. Phosphorus addition triggered divergent responses in fungal community composition across both forests: characterized by an enrichment of ectomycorrhizal fungi (EMF) and a depletion of arbuscular mycorrhizal fungi (AMF). Crucially, EMF functional guilds differentiated: short-distance exploration types increased significantly, while long-distance types declined. These findings reveal that tropical rainforests adapt to P limitation through microbially mediated strategies: enhanced soil phosphatase activity for organic P mineralization and shifts toward EMF functional groups specialized in P acquisition. Reduced PRE indicates lower reliance on internal P recycling under elevated P availability. This study underscores the importance of P availability in shaping the productivity of tropical rainforests, providing critical insights into their adaptive responses to nutrient limitations.
  • Integrated Soil Fertility Management: Aggregate carbon and nitrogen stabilization in differently textured tropical soils
    Item type: Journal Article
    Gentile, R.M.; Vanlauwe, B.; Six, Johan (2013)
    Soil Biology and Biochemistry
  • Metatranscriptomic responses of High-Arctic tundra soil microbiomes to carbon input
    Item type: Journal Article
    Varliero, Gilda; Frossard, Aline; Qi, Weihong; et al. (2024)
    Soil Biology and Biochemistry
    Over recent decades, there has been a noticeable change in vegetation diversity accompanied by increased plant productivity in tundra systems of the High-Arctic, leading to elevated carbon and nutrient inputs into the soil. This shift can alter microbial community composition and activity in these ecosystems. In this study, we aimed to identify genes transcribed by active microorganisms and compare their expression in unamended and amended soils with labile carbon and/or nitrogen compounds. We also assessed gene expression differences in tundra soils with varying edaphic characteristics (upslope vs. downslope sites). We amended soils with either glycine or cellulose or left them unamended (i.e., control) for 7 days of incubation, and we isolated and sequenced RNA using Illumina technology. Whereas we observed only a weak transcriptional response after cellulose addition, the glycine addition significantly influenced transcriptional patterns, with upregulation of carbon- and nitrogen-cycling genes. Notably, microbial taxa from the Pseudomonadaceae and Micrococcaceae families showed the most pronounced response to glycine, indicating a shift of the communities towards copiotrophic organisms. This response was consistent across the two soil types, suggesting a common impact on microbial community activity. These findings suggest that an increase in carbon and nitrogen inputs could substantially affect microbial functioning in High-Arctic tundra soils, with potential implications for ecosystem dynamics under global warming.
  • Soil metaproteomics – Comparative evaluation of protein extraction protocols
    Item type: Journal Article
    Keiblinger, Katharina M.; Wilhartitz, Inés C.; Schneider, Thomas; et al. (2012)
    Soil Biology and Biochemistry
    Metaproteomics and its potential applications are very promising to study microbial activity in environmental samples and to obtain a deeper understanding of microbial interactions. However, due to the complexity of soil samples the exhaustive extraction of proteins is a major challenge. We compared soil protein extraction protocols in terms of their protein extraction efficiency for two different soil types. Four different protein extraction procedures were applied based on (a) SDS extraction without phenol, (b) NaOH and subsequent phenol extraction, (c) SDS–phenol extraction and (d) SDS–phenol extraction with prior washing steps. To assess the suitability of these methods for the functional analysis of the soil metaproteome, they were applied to a potting soil high in organic matter and a forest soil. Proteins were analyzed by two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC–MS/MS) and the number of unique spectra as well as the number of assigned proteins for each of the respective protocols was compared. In both soil types, extraction with SDS–phenol (c) resulted in “high” numbers of proteins. Moreover, a spiking experiment was conducted to evaluate protein recovery. To this end sterilized forest soil was amended with proteins from pure cultures of Pectobacterium carotovorum and Aspergillus nidulans. The protein recovery in the spiking experiment was almost 50%. Our study demonstrates that a critical evaluation of the extraction protocol is crucial for the quality of the metaproteomics data, especially in highly complex samples like natural soils.
  • Linking soil engineers, structural stability, and organic matter allocation to unravel soil carbon responses to land-use change
    Item type: Journal Article
    Franco, André L.C.; Cherubin, Maurício R.; Cerri, Carlos E.P.; et al. (2020)
    Soil Biology and Biochemistry
    Land use changes (LUC) for the expansion of bioenergy cropping have caused consistent reductions in soil organic carbon (SOC) stocks in tropical soils. This study addresses the mechanisms underlying such SOC losses by assessing LUC effects on, and relationships between, soil engineering invertebrate fauna, soil structural stability, and C allocation and sequestration within soil aggregates. We sampled three sites with sets of land use types varying in the level of anthropogenic stress in sandy loam, sand clay loam, and clay soils along a 1000-km-long transect in central Brazil, where bioenergy cropping expands across pasturelands. We quantified the effects of LUC on soil engineer fauna (i.e., termites, earthworms, coleopterans, and ants), soil structural stability, and C allocation and fitted structural equation models (SEM) to elucidate mechanistic links between the measured variables. We found that reductions in SOC stocks following LUC were concomitant with reductions in the abundance of soil engineers (log abundance of soil engineers, −1.17 ± 0.54; P = 0.0322), destabilization of soil structure (normalized stability index, −0.16 ± 0.04; P < 0.0001), and soil depth-dependent decreases in the amounts and increases in the humification degree of aggregate-occluded SOC. Our SEMsupported the predicted relationships among these responses, and indicated that soil engineering by invertebrates indirectly mediated changes in SOC stocks across land uses by controlling the physical protection of low-humified, aggregate-occluded SOC, a C fraction that accounted for over 90% of the change in total SOC stocks following LUC. When analysing the influence of the different invertebrate groups separately, we found stronger support for the role of termites in this process compared to that of earthworms, coleopterans, and ants. Hence, negative LUC effects on populations of soil engineers weaken soil functioning and its C storage. These results highlight the need for land-use strategies that maintain soil fauna in order to sustain key ecosystem processes like soil structural formation and soil C stabilization. © 2020 Elsevier Ltd.
  • Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by vineyard management
    Item type: Journal Article
    Burns, Kayla N.; Bokulich, Nicholas; Cantu, Dario; et al. (2016)
    Soil Biology and Biochemistry
    Little is known about the hierarchical effects of management practices, soil attributes and location factors on structure of vineyard soil microbiota. A hierarchical effect occurs when the specific influence of an experimental factor (e.g. cover crop type, compost application) on soil-borne bacterial communities is greater within a subset composing the larger set but not across the entire set (e.g. bacterial communities only respond to a management practice within a subset of soil types but not across the entire set composed of all soil types). To address this concept, we measured differences in soil bacterial and archaeal diversity in wine-grape vineyard soils throughout Napa Valley, California. We describe how vineyard management practices influence soil resources, which in turn determine shifts in soil-borne bacterial communities. Soil bacterial communities were structured with respect to management practices, specifically cover crop presence and cover crop mix, tillage, and agricultural system designation, i.e. conventional, organic and biodynamic production systems. Distinctions with respect to management were associated with differences in pH and soil resource pools: total carbon and total nitrogen of the <53 and 53–250 μm particulate organic matter fractions, and potentially mineralizable nitrogen. Findings in this study suggest management practices in vineyard production systems directly influence soil microbial community structure, as mediated by shifts in soil resource pools. However, hierarchical effects occur, in which β-diversity is more strongly affected by specific management practices only within certain soil types, tillage or no-till soils or winegrowing region. This work allows for subsequent assessments of interrelationships of vineyard management, microbial biodiversity and their combined influence on soil quality, vine health, and berry quality.
  • The spatial distribution of soil microbial necromass affects nutrient mobilization and beech nutrition on silicate and calcareous forest soils
    Item type: Journal Article
    Loeppmann, Sebastian; Schmitt, Marius; Jarosch, Klaus; et al. (2025)
    Soil Biology and Biochemistry
    Only a little information is available about how the spatial heterogeneity (homogenous vs. patchy distribution) of microbial necromass affects microbial and plant phosphorus (P) and nitrogen (N) nutrition in the rhizosphere of forest soils. Therefore, a rhizotron experiment using soil from two silicate and one calcareous forest site of contrasting nutrient scarcity and P forms was conducted to investigate N and P uptake strategies of microbes and Fagus sylvatica [L.] roots depending on (i) site-specific physico-chemical properties and (ii) availability of 33P and 15N-labeled microbial necromass. The microbial necromass 33P uptake into soil microbial biomass and beech leaves decreased with increasing heterogeneity of necromass. This indicates an improved mobilization of P with a homogeneous necromass distribution especially for P-deficient silicate and calcareous soil. This was in line with increasing effect sizes of alkaline phosphatase activity with rising heterogeneity of microbial necromass. Moreover, we demonstrate site-specific N and P mobilization patterns. Up to 2-fold higher enrichment of residue-derived 15N in leaves and stems for the calcareous than for the silicate soils which reflected a faster mobilization, farther transportation, and greater distribution of 15N into the above-ground biomass, indicating an enhanced beech N nutrition. The different mechanisms governing small-scale necromass N and P distribution are affecting nutrient acquisition strategies of plants and of soil microorganisms in temperate forest ecosystems.
Publications1 - 10 of 123