Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

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Properties of Thermobifida fusca peroxidase Tfu-1649 and its combined synergistic effects with xylanase on lignocellulose degradation

BioResources ◽

10.15376/biores.16.1.942-953 ◽

2020 ◽

Vol 16 (1) ◽

pp. 942-953

Author(s):

Wan-Yu Liao ◽

Yu-Chun Huang ◽

Wei-Lin Chen ◽

Cheng-Yu Chen ◽

Chao-Hsun Yang

Keyword(s):

Reducing Sugars ◽

Plant Biomass ◽

Synergistic Effects ◽

Culture Broth ◽

Lignocellulose Degradation ◽

Total Phenolic ◽

Thermobifida Fusca ◽

Zizania Latifolia ◽

Thermophilic Actinomycetes ◽

Biomass Decomposition

Lignocelluloses are comprised of cellulose, hemicellulose, and lignins, which constitute plant biomass. Since peroxidases can degrade lignins, the authors examined peroxidase Tfu-1649, which is secreted from the thermophilic actinomycetes, Thermobifida fusca BCRC 19214. After cultivating for 48 h, the culture broth accumulated 43.66 U/mL of peroxidase activity. The treatment of four types of lignocellulolytic byproducts, i.e., bagasse, corncob, pin sawdust, and Zizania latifolia Turcz husk, with Tfu-1649 alone increased the total phenolic compounds, with limited reducing sugars, but treatment with xylanase, Tfu-11, and peroxidase Tfu-1649 showed synergistic effects. Hence, the co-operative degradation of lignocelluloses by both peroxidase and xylanase could contribute to biomass decomposition and further applications in the agricultural and environmental industries.

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Effect of Microbial Inoculants on Plant Attributes and Nutrients Uptake by Soybean in Vertisols

International Journal of Plant & Soil Science ◽

10.9734/ijpss/2021/v33i1830580 ◽

2021 ◽

pp. 102-109

Author(s):

Sanjeet Kumar ◽

R. K. Sahu ◽

R. K. Thakur ◽

Bablu Yaduwanshi ◽

N. G. Mitra

Keyword(s):

Crop Production ◽

Plant Biomass ◽

Block Design ◽

Soil Health ◽

Microbial Consortia ◽

Microbial Inoculants ◽

Randomized Block Design ◽

Nutrients Uptake ◽

Agricultural Chemistry ◽

Plant Attributes

The present study was carried out during kharif season 2019-20 at the Research Farm, Department of Soil Science & Agricultural Chemistry, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh (INDIA), to assess the effect of microbial inoculants on plant attributes and nutrients uptake by soybean in Vertisols. The experiment was laid out under randomized block design (RBD) with three replications. The 15 treatments comprised of different beneficial microbial consortia in possible combinations applied as seed treatments. The crop was supplemented with recommended dose of fertilizers 20 N : 80 P2O5 : 20 K2O kg ha-1. Besides these, two control plots were maintained as fertilized un-inoculated control (FUI) and unfertilized un-inoculated control (UFUI). The findings revealed that the significant improvement were noticed by the application of consortia NPK+EM+PGPR in plant growth attributes of nodulation at 25, 45 & 65 DAS (71, 70 & 59% respectively), over control (9.5, 33.4 & 34.7 nodule plant-1) and its biomass, (62, 69 & 74% respectively),over the control (0.58, 1.16 & 0.99 g plant-1), plant height at 25, 45 & 65DAS were increased 61, 40, 41% respectively, over the control (16.20, 34.90 and 44.30 cm) and plant biomass, (48, 62 & 53%), over the control 1.67, 4.73 and 6.1 g plant-1. Similarly, nutrient uptake (seed & stover) were also increased at 25, 45 and 65 stages of crop growth, with 36.6, 34.8 & 51.3% in seed and 66.7, 98.2 & 67.2% in straw respectively over the control (98.5, 63.8, 5.2, and 7.4, 24.9 and 44.4 kg ha-1 respectively). Thus, it may be concluded that the consortium of NPK + EM + PGPR was superior for sustainable crop production and soil health.

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The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion

10.1101/2021.01.13.426627 ◽

2021 ◽

Author(s):

Felix Schalk ◽

Cene Gostinčar ◽

Nina B. Kreuzenbeck ◽

Benjamin H. Conlon ◽

Elisabeth Sommerwerk ◽

...

Keyword(s):

Plant Biomass ◽

Biomass Conversion ◽

Degradation Mechanism ◽

Oxidative Degradation ◽

Ligninolytic Enzymes ◽

Brown Rot ◽

Dicarboxylic Acids ◽

Lignocellulose Degradation ◽

Redox Shuttle ◽

Phenolic Polymer

AbstractMacrotermitine termites have domesticated fungi in the genus Termitomyces as their primary food source using pre-digested plant biomass. To access the full nutritional value of lignin-enriched plant biomass, the termite-fungus symbiosis requires the depolymerization of this complex phenolic polymer. While most previous work suggests that lignocellulose degradation is accomplished predominantly by the fungal cultivar, our current understanding of the underlying biomolecular mechanisms remains rudimentary. Here, we provide conclusive OMICs and activity-based evidence that Termitomyces partially depolymerizes lignocellulose through the combined actions of high-redox potential oxidizing enzymes (laccases, aryl-alcohol oxidases and a manganese peroxidase), the production of extracellular H2O2 and Fenton-based oxidative degradation, which is catalyzed by a newly described 2-methoxybenzoquinone/hydroquinone redox shuttle system and mediated by secreted chelating dicarboxylic acids. In combination, our approaches reveal a comprehensive depiction of how the efficient biomass degradation mechanism in this ancient insect agricultural symbiosis is accomplished through a combination of white- and brown-rot mechanisms.ImportanceFungus-growing termites have perfected the decomposition of recalcitrant plant biomass to access valuable nutrients by engaging in a tripartite symbiosis with complementary contributions from a fungal mutualist and a co-diversified gut microbiome. This complex symbiotic interplay makes them one of the most successful and important decomposers for carbon cycling in Old World ecosystems. To date, most research has focused on the enzymatic contributions of microbial partners to carbohydrate decomposition. Here we provide genomic, transcriptomic and enzymatic evidence that Termitomyces also employs redox mechanisms, including diverse ligninolytic enzymes and a Fenton-based hydroquinone-catalyzed lignin-degradation mechanism, to break down lignin-rich plant material. Insights into these efficient decomposition mechanisms open new sources of efficient ligninolytic agents applicable for energy generation from renewable sources.

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Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production

Frontiers in Plant Science ◽

10.3389/fpls.2021.683658 ◽

2021 ◽

Vol 12 ◽

Author(s):

Caio Augusto Yoshiura ◽

Andressa Monteiro Venturini ◽

Lucas Palma Perez Braga ◽

Aline Giovana da França ◽

Maria do Carmo Catanho Pereira de Lyra ◽

...

Keyword(s):

Greenhouse Gas ◽

Biomass Production ◽

Plant Biomass ◽

Control Plant ◽

Ghg Emissions ◽

Control Treatment ◽

Lignocellulose Degradation ◽

Microbial Composition ◽

Maize Stover ◽

Plant Biomass Production

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.

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Physiological Characteristics and Comparative Secretome Analysis of Morchella importuna Grown on Glucose, Rice Straw, Sawdust, Wheat Grain, and MIX Substrates

Frontiers in Microbiology ◽

10.3389/fmicb.2021.636344 ◽

2021 ◽

Vol 12 ◽

Author(s):

YingLi Cai ◽

XiaoLong Ma ◽

QianQian Zhang ◽

FuQiang Yu ◽

Qi Zhao ◽

...

Keyword(s):

Rice Straw ◽

Lignin Degradation ◽

Extracellular Enzymes ◽

Plant Biomass ◽

Growth Potential ◽

Glycoside Hydrolases ◽

Lignocellulose Degradation ◽

Wheat Grain ◽

Predominant Component ◽

Morchella Importuna

Morels (Morchella sp.) are economically important edible macro-fungi, which can grow on various synthetic or semi-synthetic media. However, the complex nutritional metabolism and requirements of these fungi remain ill-defined. This study, based on the plant biomass commonly used in the artificial cultivation of morels, assessed and compared the growth characteristics and extracellular enzymes of Morchella importuna cultivated on glucose, rice straw, sawdust, wheat grain, and a mixture of equal proportions of the three latter plant substrates (MIX). M. importuna could grow on all five tested media but displayed significant variations in mycelial growth rate, biomass, and sclerotium yield on the different media. The most suitable medium for M. importuna was wheat and wheat-containing medium, followed by glucose, while rice straw and sawdust were the least suitable. A total of 268 secretory proteins were identified by liquid chromatography coupled with tandem mass spectrometry detection. Functional classification and label-free comparative analysis of these proteins revealed that carbohydrate-active enzyme (CAZYme) proteins were the predominant component of the secretome of M. importuna, followed by protease, peptidase, and other proteins. The abundances of CAZYme proteins differed among the tested media, ranging from 64% on glucose to 88% on rice straw. The CAZYme classes of glycoside hydrolases and carbohydrate-binding module were enriched in the five secretomes. Furthermore, the enzyme activities of CMCase, lignase, amylase, xylase, pNPCase, and pNPGase were detected during the continuous culture of M. importuna in MIX medium, and the relative expression of the corresponding genes were detected by quantitative real-time PCR. The combined data of growth potential, secretome, extracellular enzyme activity, and gene expression on different substrates inferred that M. importuna was weak in lignocellulose degradation but a good starch decomposer. Specifically, in terms of the degradation of cellulose, the ability to degrade cellulose into oligosaccharides was weaker compared with further degradation into monosaccharides, and this might be the speed-limiting step of cellulose utilization in M. importuna. In addition, M. importuna had a strong ability to decompose various hemicellulose glycosidic bonds, especially α- and β-galactosidase. Only a very few lignin-degradation-related proteins were detected, and these were in low abundance, consistent with the presence of weak lignin degradation ability. Furthermore, the presence of lipase and chitinase implied that M. importuna was capable of decomposition of its own mycelia in vitro. The study provides key data that facilitates a further understanding of the complex nutritional metabolism of M. importuna.

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Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Nature Microbiology ◽

10.1038/s41564-020-00861-0 ◽

2021 ◽

Author(s):

Xuefeng Peng ◽

St. Elmo Wilken ◽

Thomas S. Lankiewicz ◽

Sean P. Gilmore ◽

Jennifer L. Brown ◽

...

Keyword(s):

Plant Biomass ◽

Cellulose Degradation ◽

Anaerobic Bacteria ◽

Short Chain Fatty Acids ◽

Division Of Labour ◽

Microbial Consortia ◽

Bacterial Consortia ◽

Green Biotechnology ◽

Enrichment Experiments ◽

Bacteria And Fungi

AbstractThe herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

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Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Microorganisms ◽

10.3390/microorganisms10010071 ◽

2021 ◽

Vol 10 (1) ◽

pp. 71

Author(s):

Xiaofeng Wu ◽

Chijioke O. Elekwachi ◽

Shiping Bai ◽

Yuheng Luo ◽

Keying Zhang ◽

...

Keyword(s):

Microbial Community ◽

Plant Biomass ◽

High Arctic ◽

Glycoside Hydrolases ◽

Microbial Consortia ◽

Biomass Hydrolysis ◽

Host Animal ◽

Ovibos Moschatus ◽

Plant Polysaccharide ◽

Rumen Microbiome

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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