The millimetre-scale distribution of 2,4-D and its degraders drives the fate of 2,4-D at the soil core scale

Pinheiro, Marc; Garnier, Patricia; Beguet, Jérémy; Martin-Laurent, Fabrice; Gonod, Laure Vieublé

doi:10.1016/j.soilbio.2015.05.008

Cited by 30 publications

(39 citation statements)

References 58 publications

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“…A heterogeneous distribution of the cells concentrated at the inoculation point clearly limited bacterial population growth and biodegradation efficiency compared to the situation with a homogeneous distribution of bacterial cells in liquid cultures. This is in line with studies on 2,4-D biodegradation in soil columns showing that biodegradation is most efficient if degraders are uniformly dispersed (Pallud et al, 2004 ; Pinheiro et al, 2015 ). By systematically decreasing the heterogeneity of the spatial degrader distribution, Dechesne et al ( 2010a ) also found a clear improvement of benzoate mineralization.…”

Section: Discussionsupporting

confidence: 87%

“…Owing to intensive work on spatial heterogeneity in soil, the endemism hypothesis for bacteria is now generally accepted (Cho and Tiedje, 2000 ; Fulthorpe et al, 2008 ) and there is increasing awareness that heterogeneity is not only a field-scale phenomenon, but similarly occurs at the micro-scale (Vieublé Gonod et al, 2006 ). Studies on the distribution of 2,4-dichlorophenoxyacetic acid (2,4-D) degraders in soil and soil column systems confirmed the existence of soil regions comprising several millimeters right up to a few centimeters, which are devoid of 2,4-D degrading activity (Pallud et al, 2004 ; Vieublé Gonod et al, 2006 ; Pinheiro et al, 2015 ). However, the majority of publications dealing with spatial heterogeneity of bacterial degraders in soils are rather descriptive, whereas the consequences of these small-scale spatial heterogeneities on biodegradation efficiency are difficult to assess and thus have hardly been evaluated so far (Dechesne et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

et al. 2016

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Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. Here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of osmotic potentials (ΔΨo) using model ecosystems exhibiting a heterogeneous distribution of the soil-borne bacterium Pseudomonas putida KT2440. Three systematically manipulated scenarios allowed us to cover the effects of (i) substrate diffusion, (ii) substrate diffusion and autonomous bacterial dispersal, and (iii) substrate diffusion and autonomous as well as mediated bacterial dispersal along glass fiber networks mimicking fungal hyphae. To quantify the relative importance of the different spatial processes, we compared these heterogeneous scenarios to a reference value obtained for each ΔΨo by means of a quasi-optimal scenario in which degraders were ab initio homogeneously distributed. Substrate diffusion as the sole spatial process was insufficient to counteract the disadvantage due to spatial degrader heterogeneity at ΔΨo ranging from 0 to −1 MPa. In this scenario, only 13.8−21.3% of the quasi-optimal biodegradation performance could be achieved. In the same range of ΔΨo values, substrate diffusion in combination with bacterial dispersal allowed between 68.6 and 36.2% of the performance showing a clear downwards trend with decreasing ΔΨo. At −1.5 MPa, however, this scenario performed worse than the diffusion scenario, possibly as a result of energetic disadvantages associated with flagellum synthesis and emerging requirements to exceed a critical population density to resist osmotic stress. Network-mediated bacterial dispersal kept biodegradation almost consistently high with an average of 70.7 ± 7.8%, regardless of the strength of the osmotic stress. We propose that especially fungal network-mediated bacterial dispersal is a key process to achieve high functionality of heterogeneous microbial ecosystems also at reduced osmotic potentials. Thus, mechanical stress by, for example, soil homogenization should be kept low in order to preserve fungal network integrity.

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Section: Discussionsupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

et al. 2016

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“…Root growth, root development and deposition of root exudates were therefore as close to natural conditions as possible. The separation or colocalization of microbes and substrates has been shown to be critical for carbon turnover on a small scale (Pinheiro et al, 2015) and is a so far underestimated factor in studies using homogenized soil solely.…”

Section: Discussionmentioning

confidence: 99%

Bacteria utilizing plant‐derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Uksa

Buegger

Gschwendtner

et al. 2017

Environ Microbiol Rep

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Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, C-CO labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

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“…Nanoscale secondary ion mass spectrometry (nanoSIMS) and synchrotron radiation [scanning transmission x-ray microscope (STXM) and near edge x-ray absorption fine structure (NEXAFS)] imaging can locate OM and microorganisms at the micrometre scale, while also providing chemical information complementary to that obtained through fluorescence microscopy studies of thin soil sections (Raynaud and Nunan 2014). It has been shown that OM-decomposer co-localisation accelerates biodegradation (Vieublé Gonod et al 2003;Pinheiro et al 2015;Don et al 2013), while accessibility of OM to microbes might be a major driver of soil C dynamics (Dungait et al 2012). This contact can occur by substrate and enzyme diffusion and advection, or via microorganism growth and mobility (Fig.…”

Section: Localisation In the Physical Structure Of Soilmentioning

confidence: 99%

Increasing soil carbon storage: mechanisms, effects of agricultural practices and proxies. A review

Dignac

Derrien

Barré

et al. 2017

Agron. Sustain. Dev.

Self Cite

366

170

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The international 4 per 1000 initiative aims at supporting states and non-governmental stakeholders in their efforts towards a better management of soil carbon (C) stocks. These stocks depend on soil C inputs and outputs. They are the result of fine spatial scale interconnected mechanisms, which stabilise/destabilise organic matter-borne C. Since 2016, the CarboSMS consortium federates French researchers working on these mechanisms and their effects on C stocks in a local and global change setting (land use, agricultural practices, climatic and soil conditions, etc.). This article is a synthesis of this consortium's first seminar. In the first part, we present recent advances in the understanding of soil C stabilisation mechanisms comprising biotic and abiotic processes, which occur concomitantly and interact. Soil organic C stocks are altered by biotic activities of plants (the main source of C through litter and root systems), microorganisms (fungi and bacteria) and 'ecosystem engineers' (earthworms, termites, ants). In the meantime, abiotic processes related to the soil-physical structure, porosity and mineral fraction also modify these stocks. In the second part, we show how agricultural practices affect soil C stocks. By acting on both biotic and abiotic mechanisms, land use and management practices This synthesis of the CarboSMS French consortium's first seminar was already published in French: Derrien D, Dignac M-F, Basile-Doelsch I, Barot S, Cécillon L, Chenu C, Chevallier T, Freschet GT, Garnier P, Guenet B, Hedde M, Klumpp K, Lashermes G, Maron P-A, Nunan N, Roumet C, Barré P (2016) (choice of plant species and density, plant residue exports, amendments, fertilisation, tillage, etc.) drive soil spatiotemporal organic inputs and organic matter sensitivity to mineralisation. Interaction between the different mechanisms and their effects on C stocks are revealed by meta-analyses and long-term field studies. The third part addresses upscaling issues. This is a cause for major concern since soil organic C stabilisation mechanisms are most often studied at fine spatial scales (mm-μm) under controlled conditions, while agricultural practices are implemented at the plot scale. We discuss some proxies and models describing specific mechanisms and their action in different soil and climatic contexts and show how they should be taken into account in large scale models, to improve change predictions in soil C stocks. Finally, this literature review highlights some future research prospects geared towards preserving or even increasing C stocks, our focus being put on the mechanisms, the effects of agricultural practices on them and C stock prediction models.

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The millimetre-scale distribution of 2,4-D and its degraders drives the fate of 2,4-D at the soil core scale

Cited by 30 publications

References 58 publications

Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

Bacteria utilizing plant‐derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Increasing soil carbon storage: mechanisms, effects of agricultural practices and proxies. A review

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