Journal: Soil Biology and Biochemistry

Abbreviation

Soil biol. biochem.

Publisher

Elsevier

Journal Volumes

ISSN

0038-0717
1879-3428

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Publications 1 - 10 of 123
  • 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
  • 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.
  • A coupled function of biochar as geobattery and geoconductor leads to stimulation of microbial Fe(III) reduction and methanogenesis in a paddy soil enrichment culture
    Item type: Journal Article
    Yang, Zhen; Sun, Tianran; Kleindienst, Sara; et al. (2021)
    Soil Biology and Biochemistry
    Biochar can participate in biogeochemical electron transfer processes due to its electron-accepting and donating capabilities (i.e., geobattery) and electron conductivity (i.e., geoconductor). These two functions were separately demonstrated to play a role in biogeochemical iron cycling and methane formation. Yet, little is known about the coupled effect of both electron transfer mechanisms, even though naturally occurring electron transfer through biochar is expected to simultaneously rely on both geobattery and geoconductor mechanisms. Here, we incubated an anoxic paddy soil enrichment culture with acetate as the substrate to investigate how biochar's coupled electron transfer mechanisms influence the electron transfer pathways between microbes and Fe(III) minerals and how it impacts the soil microbial community composition. We found that biochar simultaneously stimulated microbial Fe(III) reduction and methanogenesis by 2.6 and 2.3 fold, but these processes were spatially decoupled. Small biochar particles (5–20 μm) caused higher Fe(III) reduction and methanogenesis rates than large particles (50–100 μm). The addition of biochar enriched a syntrophic acetate-oxidizing co-culture with dominating Fe(III)-reducing Geobacteraceae taxa and acetoclastic methanogenic Methanosarcina taxa. After acetoclastic methanogenesis stopped, the observed continuing methanogenesis was likely due to interspecies electron transfer caused by biochar functioning as a geoconductor transferring electrons from Geobacteraceae to Methanosarcina. In summary, the simultaneous occurrence of Fe(III) reduction and methanogenesis leads to the formation of a cell-biochar-mineral battery network and a cell-biochar-cell conductive network in an enrichment culture from a paddy soil.
  • 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.
  • Distinct responses of soil fungal and bacterial nitrate immobilization to land conversion from forest to agriculture
    Item type: Journal Article
    Li, Xiaobo; He, Hongbo; Zhang, Xudong; et al. (2019)
    Soil Biology and Biochemistry
  • Microplastics in agricultural soils: The role of soil texture in modulating oxygen diffusivity and soil respiration
    Item type: Journal Article
    Nuñez, Jonathan; Jimenez-Martinez, Joaquin; Carminati, Andrea; et al. (2025)
    Soil Biology and Biochemistry
    The presence of microplastics (MPs) in soils impacts nutrient cycling and soil respiration. However, the mechanisms underpinning the direction and magnitude of these effects on soil are uncertain. We hypothesized that the presence of MPs affects pore connectivity, leading to changes in oxygen (O2) diffusivity and soil respiration. Furthermore, we anticipated that the magnitude of the effects would be dependent on both soil texture and MPs morphology. 1 % (w/w) PET MPs fibers (500 μm length) and fragments (125–250 μm) were spiked into rhizotrons filled with either clay or sandy loam soils. O2 diffusivity differences were determined in microcosm using an oxygen-free chamber. The O2 concentration in the soil was also measured in optimal conditions for respiration. O2 diffusivity and concentration were measured using optode imaging. Respiration was estimated from cumulative CO2 and changes in the size of the water-extractable carbon pool. Adding MPs decreased O2 concentration in the sandy loam soil (167.4 ± 6.1 mg L−1 air), with a greater reduction observed for fragments (15 %) compared to fibers (12 %). Soil respiration decreased by 40 % in both fragment and fiber treatments in alignment with the reduction in oxygen concentration. Conversely, in the clay soil, the addition of fibers and fragments resulted in a 13 and 7 % increase in O2 concentration compared to the control (177.9 ± 3.8 mg L−1 air). Both changes in oxygen concentration and diffusivity, show a similar response to MPs for the two soils. These findings indicate that the effects of MPs on soil respiration are likely driven by changes in O2 dynamics. However, the MPs' impact on O2 dynamics depends on soil particle size distribution. Future research should consider MP size, morphology, and soil particle distribution interactions to assess MPs' impacts on soil functions.
  • Carbon pulses but not phosphorus pulses are related to decreases in microbial biomass during repeated drying and rewetting of soils
    Item type: Journal Article
    Butterly, Clayton R.; Bünemann, Else K.; McNeill, Ann M.; et al. (2009)
    Soil Biology and Biochemistry
    Drying and rewetting cycles are known to be important for the turnover of carbon (C) in soil, but less is known about the turnover of phosphorus (P) and its relation to C cycling. In this study the effects of repeated drying-rewetting (DRW) cycles on phosphorus (P) and carbon (C) pulses and microbial biomass were investigated. Soil (Chromic Luvisol) was amended with different C substrates (glucose, cellulose, starch; 2.5 g C kg−1) to manipulate the size and community composition of the microbial biomass, thereby altering P mineralisation and immobilisation and the forms and availability of P. Subsequently, soils were either subjected to three DRW cycles (1 week dry/1 week moist) or incubated at constant water content (70% water filled pore space). Rewetting dry soil always produced an immediate pulse in respiration, between 2 and 10 times the basal rates of the moist incubated controls, but respiration pulses decreased with consecutive DRW cycles. DRW increased total CO2 production in glucose and starch amended and non-amended soils, but decreased it in cellulose amended soil. Large differences between the soils persisted when respiration was expressed per unit of microbial biomass. In all soils, a large reduction in microbial biomass (C and P) occurred after the first DRW event, and microbial C and P remained lower than in the moist control. Pulses in extractable organic C (EOC) after rewetting were related to changes in microbial C only during the first DRW cycle; EOC concentrations were similar in all soils despite large differences in microbial C and respiration rates. Up to 7 mg kg−1 of resin extractable P (Presin) was released after rewetting, representing a 35–40% increase in P availability. However, the pulse in Presin had disappeared after 7 d of moist incubation. Unlike respiration and reductions in microbial P due to DRW, pulses in Presin increased during subsequent DRW cycles, indicating that the source of the P pulse was probably not the microbial biomass. Microbial community composition as indicated by fatty acid methyl ester (FAME) analysis showed that in amended soils, DRW resulted in a reduction in fungi and an increase in Gram-positive bacteria. In contrast, the microbial community in the non-amended soil was not altered by DRW. The non-selective reduction in the microbial community in the non-amended soil suggests that indigenous microbial communities may be more resilient to DRW. In conclusion, DRW cycles result in C and P pulses and alter the microbial community composition. Carbon pulses but not phosphorus pulses are related to changes in microbial biomass. The transient pulses in available P could be important for P availability in soils under Mediterranean climates.
  • Assessment of gross and net mineralization rates of soil organic phosphorus: A review
    Item type: Review Article
    Bünemann, Else K. (2015)
    Soil Biology and Biochemistry
  • Compound-specific amino acid ¹⁵N-stable isotope probing for the quantification of biological nitrogen fixation in soils
    Item type: Journal Article
    Chiewattanakul, Mashita; McAleer, Adam D.A.; Reay, Michaela K.; et al. (2022)
    Soil Biology and Biochemistry
    Biological nitrogen fixation (BNF) performed by diazotrophs is vital to our understanding of ecosystem functions, as plant nitrogen (N) is commonly a limiting nutrient for primary productivity. However, significant limitations have remained in our knowledge of the controls and rates of this process, due to technical difficulties in directly quantifying nitrogen (N2) fixation rates. To address this, we developed a novel compound-specific 15N-stable isotope probing method involving analysis of acid hydrolysable soil amino acids (AAs) by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the quantification of BNF in soils. By analysing 15N-enriched AAs (as N-acetyl, O-isopropyl derivatives), this new approach aimed to provide greater specificity compared to existing methods, and to contribute previously unobtainable quantitative information on the capture and flow of N2 fixed in soils. Laboratory incubations using 15N2 gas were carried out on surface peat over 15 days to obtain quantitative measures of N2 fixation by the microbial community. Longer incubations with the addition of a glucose energy source significantly increased the level of 15N enrichment, i.e. N fixed. The enhanced detection limits of 15N-AAs by GC-C-IRMS, compared to bulk soil δ15N value determinations, was key to assessments of N2 fixation. Valuable insights into the assimilation pathway of the applied 15N2-substrate were revealed; for peat soils, 15N incorporation into glutamate dominated over other AAs.
  • Chemical changes and phosphorus release during decomposition of pea residues in soil
    Item type: Journal Article
    Ha, K.V.; Marschner, P.; Bünemann, Else K.; et al. (2007)
    Soil Biology and Biochemistry
Publications 1 - 10 of 123