Observations on two microbial life strategies in soil: Planktonic and biofilm-forming microorganisms are separable

Bystrianský, Lukáš; Hujslová, Martina; Hršelová, Hana; Řezáčová, Veronika; Němcová, Lenka; Šimsová, Jana; Gryndlerová, Hana; Kofroňová, Olga; Benada, Oldřich; Gryndler, Milan

doi:10.1016/j.soilbio.2019.107535

Cited by 23 publications

(8 citation statements)

References 63 publications

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“…Furthermore, the opacity of the soil matrix hinders microscopic observation of soil biofilms (Wu et al 2019). Soil microbes also exist as freeliving planktonic cells; however, information on the distribution and functions of each fraction is limited (Bystrianský et al 2019).…”

Section: Lignocellulose Degradation In Predominately Aerobic Ecosystemsmentioning

confidence: 99%

Impacts of biofilms on the conversion of cellulose

Brethauer

Shahab

Studer

2020

Appl Microbiol Biotechnol

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Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms-matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature-have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. Key Points & Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. & Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. & Fungal biofilms immobilize enzymes and substrates in an external digestion system. & Surface attached cultures typically show higher expression of cellulolytic enzymes.

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Section: Lignocellulose Degradation In Predominately Aerobic Ecosystemsmentioning

confidence: 99%

Impacts of biofilms on the conversion of cellulose

Brethauer

Shahab

Studer

2020

Appl Microbiol Biotechnol

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“…Among biotic factors, mainly bacteria and fungi, and especially arbuscular mycorrhizal fungi (AMF; Glomeromycotina 12 ) 11 , 13 – 15 importantly influence the stability of soil aggregates 16 – 18 . AMF and bacteria are important producers of extracellular polymeric substances that bind soil particles together 19 – 21 , maintain ambient humidity, and serve as a reserve of carbon and mineral nutrients 3 . Glomalins are AMF products of particular importance in the formation and stabilization of soil aggregates 22 , 23 .…”

Section: Introductionmentioning

confidence: 99%

Organic fertilization improves soil aggregation through increases in abundance of eubacteria and products of arbuscular mycorrhizal fungi

Řezáčová

Czakó

Stehlík

et al. 2021

Sci Rep

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An important goal of sustainable agriculture is to maintain soil quality. Soil aggregation, which can serve as a measure of soil quality, plays an important role in maintaining soil structure, fertility, and stability. The process of soil aggregation can be affected through impacts on biotic and abiotic factors. Here, we tested whether soil management involving application of organic and mineral fertilizers could significantly improve soil aggregation and if variation among differently fertilized soils could be specifically attributed to a particular biotic and/or abiotic soil parameter. In a field experiment within Central Europe, we assessed stability of 1–2 mm soil aggregates together with other parameters of soil samples from differently fertilized soils. Application of compost and digestates increased stability of soil aggregates. Most of the variation in soil aggregation caused by different fertilizers was associated with soil organic carbon lability, occurrence of aromatic functional groups, and variations in abundance of eubacteria, total glomalins, concentrations of total S, N, C, and hot water extractable C. In summary, we have shown that application of compost and digestates improves stability of soil aggregates and that this is accompanied by increased soil fertility, decomposition resistance, and abundance of total glomalins and eubacteria. These probably play significant roles in increasing stability of soil aggregates.

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“…Analogous to MSI, wide-field optical microscopy also does not deliver images with high lateral resolution. On the other hand, SEM is capable of visualizing large samples with unprecedented resolution in a complex environment and a considerable depth of field [ 9 ] to show bacterial biofilms or bacterial cell surface details such as flagella and pili [ 10 ]. However, the preparation of biological specimens for SEM may be complicated [ 11 ], and sample chemical fixation is needed for stabilization and structural preservation.…”

Section: Introductionmentioning

confidence: 99%

Bringing SEM and MSI Closer Than Ever Before: Visualizing Aspergillus and Pseudomonas Infection in the Rat Lungs

Juříková

Luptáková

Kofroňová

et al. 2020

JoF

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A procedure for processing frozen rat lung tissue sections for scanning electron microscopy (SEM) from deeply frozen samples initially collected and stored for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was developed. The procedure employed slow thawing of the frozen sections while floating on the surface and melting in a fixative solution. After the float-washing step, the sections were dehydrated in a graded ethanol series and dried in a critical point dryer. The SEM generated images with well-preserved structures, allowing for monitoring of bacterial cells and fungal hyphae in the infected tissue. Importantly, the consecutive nonfixed frozen sections were fully compatible with MALDI-MSI, providing molecular biomarker maps of Pseudomonas aeruginosa. The protocol enables bimodal image fusion in the in-house software CycloBranch, as demonstrated by SEM and MALDI-MSI.

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Observations on two microbial life strategies in soil: Planktonic and biofilm-forming microorganisms are separable

Cited by 23 publications

References 63 publications

Impacts of biofilms on the conversion of cellulose

Impacts of biofilms on the conversion of cellulose

Organic fertilization improves soil aggregation through increases in abundance of eubacteria and products of arbuscular mycorrhizal fungi

Bringing SEM and MSI Closer Than Ever Before: Visualizing Aspergillus and Pseudomonas Infection in the Rat Lungs

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