Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

Abstract Background Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Results Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. Conclusions The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.

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Temporal dynamics and ecophysiology of thermophilic composting analyzed through metagenome-assembled genomes

10.21203/rs.3.rs-19445/v1 ◽

2020 ◽

Author(s):

João Carlos Setubal ◽

Lucas Palma Perez Braga ◽

Roberta Verciano Pereira ◽

Layla Farage Martins ◽

Livia Maria Silva Moura ◽

...

Keyword(s):

Temporal Dynamics ◽

Sulfur Metabolism ◽

Oxygen Metabolism ◽

Lignocellulose Degradation ◽

Specific Information ◽

Gene Repertoire ◽

General Description ◽

Hydrogen Metabolism ◽

Composting Process ◽

Molecular Features

Abstract Background: Thermophilic composting is a semi-engineered process carried out by diverse microbial communities. Composting is an environment friendly way of degrading biomass; its study may help uncover important biomass-degrading organisms and key enzymes. DNA sequence-based previous studies have presented a general description of the microbial-molecular features of composting, but they have lacked more specific information on the key organisms that are active during the process and their genomes. Methods: We present an analysis of metagenome-assembled genomes (MAGs) obtained from time-series samples of a thermophilic composting process in the São Paulo Zoological Park (Brazil). Our results are based on a careful analysis of MAG gene content and on metabolic modeling of their interactions. Results: We recovered 60 MAGs from sequencing datasets from two separate composting cells. Phylogenetic analysis shows that 47 of these MAGs represent novel taxa at the genus or higher levels. We have analyzed the gene repertoire of these MAGs in terms of lignocellulose degradation, secondary metabolite production, antibiotic resistance genes, denitrification genes, sulfur metabolism, hydrogen metabolism, and oxygen metabolism. For one of the composting cells we also had metatranscriptome data, which allowed a deeper analysis of 49 MAGs. This analysis showed the presence of three distinct clusters of MAGs with varying activity during the 99-day composting process. The interaction model pointed to Sphaerobacter thermophilus and Thermobispora bispora as key players in the process, as well as other bacteria that are novel. Our results also show the importance of coadjuvant bacteria and of microbial functions related to efficient bioenergetic processes during biomass conversion, such as N2O reduction and hydrogenases. A novel acidobacteria MAG encodes N2O reductase hallmark genes (nosZD). Strong metabolic dependencies predicted between MAGs revealed that cross-feeding in composting can be determined by complementary functions found in the genomes of producers and consumers, supporting the Black Queen hypothesis for co-evolutionary interactions. Conclusions: This study reveals for the first time the key bacterial players in thermophilic composting and provides a model of their dynamic metabolic interactions. These findings pave the way for more rational composting procedures and provide information that could help the development of novel biomass-degrading technologies.

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A novel Swollenin from Talaromyces leycettanus JCM12802 exhibits cellulase activity and enhanced cellulase hydrolysis towards various substrates

10.21203/rs.3.rs-22793/v1 ◽

2020 ◽

Author(s):

Honghai Zhang ◽

Yuan Wang ◽

Roman Brunecky ◽

Bin Yao ◽

Xiangming Xie ◽

...

Keyword(s):

Synergistic Effect ◽

Functional Diversity ◽

Specific Activity ◽

Biomass Conversion ◽

Hydrolytic Enzymes ◽

Cellulase Activity ◽

Industrial Applications ◽

Maximum Activity ◽

Carbohydrate Binding ◽

Cell Wall Polysaccharides

Abstract Background Swollenins are present in some fungal species involved in the biodegradation of cellulosic substrates. They appear to promote a rearrangement in the network of non-covalent interactions between the cell wall polysaccharides, thus making it more accessible for degradation by hydrolytic enzymes. Here, we have reported a detailed characterization of a recombinant swollenin with respect to its disruptive activity on cellulosic substrates and synergistic effect with cellulases. Results In the present study, a novel swollenin gene Tlswo consisting of an open reading frame encoding 503 amino acids was identified from Talaromyces leycettanus JCM12802 and successfully expressed in Trichoderma reesei and Pichia pastoris. Similar to other fungal swollenins, TlSWO contained a N-terminal family 1 carbohydrate binding module (CBM1) followed by a Ser/Thr rich linker connected to expansin-like domain which includes a family 45 endoglucanase-like domain and group-2 grass pollen allergen domain. TlSWO demonstrated disruptive activity on Avicel and displayed a high synergistic effect with cellobiohydrolases, enhancing its hydrolytic performance up to 132%. The activity of TlSWO on various substrates and biomass was also examined. It was shown that TlSWO could release reducing sugars from lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin. The specific activity of TlSWO towards the substates above is 9.0 ± 0.100 U/mg, 8.9 ± 0.100U/mg, 2.3 ± 0.002 U/mg and 0.79 ± 0.002 U/mg respectively. Moreover, TlSWO exhibits maximum activity at pH 4.0 and 50 ℃. Conclusion This study reported on a novel swollenin with highly efficient for biomass conversion. It also reveals the functional diversity of swollenin with activity on various substrates. Although the exact mechanism of swollenin catalytic action activity still remains unknown, the functional diversity of TlSWO makes it a good candidate for industrial applications.

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High functional diversity stimulates diversification in experimental microbial communities

Science Advances ◽

10.1126/sciadv.1600124 ◽

2016 ◽

Vol 2 (6) ◽

pp. e1600124 ◽

Cited By ~ 26

Author(s):

Alexandre Jousset ◽

Nico Eisenhauer ◽

Monika Merker ◽

Nicolas Mouquet ◽

Stefan Scheu

Keyword(s):

Ecosystem Services ◽

Functional Diversity ◽

Bacterial Communities ◽

Evolutionary Dynamics ◽

Resource Competition ◽

Bacterial Species ◽

Focal Species ◽

Evolutionary Diversification ◽

The Impact ◽

High Diversity

There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.

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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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Bayesian Inference for Single-cell Clustering and Imputing

Genomics and Computational Biology ◽

10.18547/gcb.2017.vol3.iss1.e46 ◽

2017 ◽

Vol 3 (1) ◽

pp. 46 ◽

Cited By ~ 25

Author(s):

Elham Azizi ◽

Sandhya Prabhakaran ◽

Ambrose Carr ◽

Dana Pe'er

Keyword(s):

Single Cell ◽

Cell Types ◽

Superior Performance ◽

Underlying Structure ◽

Specific Information ◽

Cell Type ◽

Cell Clustering ◽

Bayesian Probabilistic Model ◽

Cell Type Specific ◽

Cell Data

Single-cell RNA-seq gives access to gene expression measurements for thousands of cells, allowing discovery and characterization of cell types. However, the data is noise-prone due to experimental errors and cell type-specific biases. Current computational approaches for analyzing single-cell data involve a global normalization step which introduces incorrect biases and spurious noise and does not resolve missing data (dropouts). This can lead to misleading conclusions in downstream analyses. Moreover, a single normalization removes important cell type-specific information. We propose a data-driven model, BISCUIT, that iteratively normalizes and clusters cells, thereby separating noise from interesting biological signals. BISCUIT is a Bayesian probabilistic model that learns cell-specific parameters to intelligently drive normalization. This approach displays superior performance to global normalization followed by clustering in both synthetic and real single-cell data compared with previous methods, and allows easy interpretation and recovery of the underlying structure and cell types.

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Exploring the niche concept in a simple metaorganism

10.1101/814798 ◽

2019 ◽

Author(s):

Peter Deines ◽

Katrin Hammerschmidt ◽

Thomas CG Bosch

Keyword(s):

Community Assembly ◽

Bacterial Species ◽

Realized Niche ◽

Darwinian Fitness ◽

Host Health ◽

Species Abundances ◽

Metabolic Interactions ◽

Niche Concept ◽

The Individual ◽

Microbial Community Assembly

AbstractOrganisms and their resident microbial communities - the microbiome - form a complex and mostly stable ecosystem. It is known that the composition of the microbiome and bacterial species abundances can have a major impact on host health and Darwinian fitness, but the processes that lead to these microbial patterns have not yet been identified. We here apply the niche concept and trait-based approaches as a first step in understanding the patterns underlying microbial community assembly and structure in the simple metaorganism Hydra. We find that the carrying capacities in single associations do not reflect microbiota densities as part of the community, indicating a discrepancy between the fundamental and realized niche. Whereas in most cases, the realized niche is smaller than the fundamental one, as predicted by theory, the opposite is observed for Hydra’s two main bacterial colonizers. Both, Curvibacter sp. and Duganella sp. benefit from association with the other members of the microbiome and reach higher fractions as compared to when they are the only colonizer. This cannot be linked to any particular trait that is relevant for interacting with the host or by the utilization of specific nutrients but is most likely determined by metabolic interactions between the individual microbiome members.

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Evaluation of probiotic bacteria Leucosnostoc mensenteroides against White Gut Disease in shrimp aquaculture

Journal of University of Shanghai for Science and Technology ◽

10.51201/jusst/21/11976 ◽

2021 ◽

Vol 23 (11) ◽

pp. 891-905

Author(s):

A. Sathyapriya ◽

Keyword(s):

Bacterial Species ◽

Vibrio Anguillarum ◽

Treated Group ◽

Probiotic Bacteria ◽

Beneficial Bacteria ◽

Environment Friendly ◽

Pathogenic Vibrio ◽

Pathogen Control ◽

Increasing Demand

With increasing demand for environment friendly aquaculture, use of beneficial bacteria to displace pathogens by competitive processes is being used in the animal industry as a better remedy and is now gaining acceptance for pathogen control in aquaculture. With this concern, the present study was designed for isolation of suitable probiotic bacteria from natural sources, application in an effective dose in the rearing environment is expected to control the blowout of White Gut Disease in aquaculture systems. The interaction of pathogenic Vibrio anguillarum and the inner surface of the digestive tract of P. monodon, with a specific focus on their in-situ morphology, aggregation and attachment characteristics presented with pathogenic bacterial species and under the control of probiotic bacteria were analyzed through. The percentage of granular cells of treated group was higher than the control. Histological studies revealed that the treated group has optimistic effect which helps in the reduction of tissue damage and decrease the mortality rate than the infected shrimps. Leuconostoc sp., can survive in the saline condition rather than other Lactobacillus sp., and its tolerance of acidic environment of the shrimp intestine and their adherence level at the intestine will progressively replace the V. anguillarum from the infected shrimps and commendably control the White Gut Disease.

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Fungal mycelia and bacterial thiamine establish a mutualistic growth mechanism

Life Science Alliance ◽

10.26508/lsa.202000878 ◽

2020 ◽

Vol 3 (12) ◽

pp. e202000878 ◽

Cited By ~ 1

Author(s):

Gayan Abeysinghe ◽

Momoka Kuchira ◽

Gamon Kudo ◽

Shunsuke Masuo ◽

Akihiro Ninomiya ◽

...

Keyword(s):

Bacillus Subtilis ◽

Isotope Labeling ◽

Bacterial Species ◽

Hyphal Growth ◽

Bacterial Cells ◽

Environmental Niche ◽

Metabolic Interactions ◽

Physical Spaces ◽

Fungal Colony ◽

Fungal Mycelia

Exclusivity in physical spaces and nutrients is a prerequisite for survival of organisms, but a few species have been able to develop mutually beneficial strategies that allow them to co-habit. Here, we discovered a mutualistic mechanism between filamentous fungus, Aspergillus nidulans, and bacterium, Bacillus subtilis. The bacterial cells co-cultured with the fungus traveled along mycelia using their flagella and dispersed farther with the expansion of fungal colony, indicating that the fungal mycelia supply space for bacteria to migrate, disperse, and proliferate. Transcriptomic, genetic, molecular mass, and imaging analyses demonstrated that the bacteria reached the mycelial edge and supplied thiamine to the growing hyphae, which led to a promotion of hyphal growth. The thiamine transfer from bacteria to the thiamine non-auxotrophic fungus was directly demonstrated by stable isotope labeling. The simultaneous spatial and metabolic interactions demonstrated in this study reveal a mutualism that facilitates the communicating fungal and bacterial species to obtain an environmental niche and nutrient, respectively.

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Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species

10.1101/2020.05.15.097725 ◽

2020 ◽

Author(s):

Tony J. Lam ◽

Moses Stamboulian ◽

Wontack Han ◽

Yuzhen Ye

Keyword(s):

Microbial Communities ◽

Bacterial Species ◽

Microbial Interactions ◽

Phylogenetic Distance ◽

Phylogenetic Relatedness ◽

Bacterial Interactions ◽

Competition And Cooperation ◽

Microbial Species ◽

Metabolic Interactions ◽

Genome Scale

AbstractMicrobial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of metabolic interactions, such as competition and cooperation, between bacterial species. By nature, phylogenetically similar microbial species are likely to share common functional profiles or biological pathways due to their genomics similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation based on functional/pathway profiles may bias downstream applications.To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.Author summaryMicrobial communities, also known as microbiomes, are formed through the interactions of various microbial species. Utilizing genomic sequencing, it is possible to infer the compositional make-up of communities as well as predict their metabolic interactions. However, because some species are more similarly related to each other, while others are more distantly related, one cannot directly compare metabolic relationships without first accounting for their phylogenetic relatedness. Here we developed a computational pipeline which predicts complimentary and competitive metabolic relationships between bacterial species, while normalizing for their phylogenetic relatedness. Our results show that phylogenetic distances are correlated with metabolic interactions, and factoring out such relationships can help better understand microbial interactions which drive community formation.

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