Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction

Lillington, Stephen P.; Leggieri, Patrick A.; Heom, Kellie A.; O’Malley, Michelle

doi:10.1016/j.copbio.2019.08.015

Cited by 36 publications

(17 citation statements)

References 107 publications

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“…In contrast, anaerobic bacteria and fungi predominately express free or cell-bound complexed cellulases, where a large number of catalytic units and CMBs are bound to a scaffold backbone and form a cellulosome. Substrate channeling in cellulosomes has been shown to enhance the cellulolytic activity over free enzymes by a factor of 12 (Lillington et al 2019).…”

Section: Resultsmentioning

confidence: 99%

“…Anaerobic gut fungi-Neocallimastigomycota-account for up to 8% of the microbial mass of the gut (Hooker et al 2019;Theodorou et al 1996) and are the primary microbes colonizing plant biomass while the other microbiota are getting involved later (Haitjema et al 2014;Orpin 1975). Anaerobic gut fungi degrade untreated biomass through invasive growth of their rhizomycelium into and through the particles (Lillington et al 2019) and are able to solubilize 40 to 70% of lignocellulose in 4 days in in vitro digestion experiments employing rumen fluid supplemented with antibiotics (Akin and Rigsby 1987). Some isolated strains grew on nonpretreated grasses at rates comparable or even higher to the ones on soluble substrates (Solomon et al 2016).…”

Section: Lignocellulose Degradation In Predominately Anaerobic Ecosysmentioning

confidence: 99%

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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: Resultsmentioning

confidence: 99%

Section: Lignocellulose Degradation In Predominately Anaerobic Ecosysmentioning

confidence: 99%

Impacts of biofilms on the conversion of cellulose

Brethauer

Shahab

Studer

2020

Appl Microbiol Biotechnol

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“…Acidobacter also plays an important role in polymer degradation and other aspects, including Granulicella as a representative (Pankratov and Dedysh, 2010). Lillington et al (2020) found that anaerobic microbial communities can degrade and promote the carbon cycle on Earth.…”

Section: Discussionmentioning

confidence: 99%

Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China

Shang

Wei

et al. 2020

Front. Microbiol.

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Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA highthroughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO 4 2−)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.

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“…Spatial heterogeneity can be incorporated into community GEMs (153,157,158), typically by means of FBA to find each species' growth rate at each time step in numerical solutions of reactiondiffusion partial differential equations (159). Biofilms, in particular, are increasingly being modeled with spatiotemporal GEMs (21,158,160,161).…”

Section: Dynamic Models Of Microbiome Fluxmentioning

confidence: 99%

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Leggieri

Liu

Hayes

et al. 2021

Annu. Rev. Biomed. Eng.

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Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction

Cited by 36 publications

References 107 publications

Impacts of biofilms on the conversion of cellulose

Impacts of biofilms on the conversion of cellulose

Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

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