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Expression of lignocellulolytic glycoside hydrolase families in enriched mesophilic and thermophilic microbial communities % of lignocellulolytic GH transcriptome *
Source publication
New lignocellulolytic enzymes are needed that maintain optimal activity under the harsh conditions present during industrial enzymatic deconstruction of biomass, including high temperatures, the absence of free water, and the presence of inhibitors from the biomass. Enriching lignocellulolytic microbial communities under these conditions provides a...
Context in source publication
Context 1
... data for sequences annotated with lignocel- lulolytic glycoside hydrolase (GH) Pfams (Table 2) show differing profiles in the GHs produced by enriched thermophilic and mesophilic communities (Table 3). The majority of cellulase expression in the thermophilic community corresponded to GH families 6, 9, and 48. ...
Citations
... Specific members of these communities, especially bacterial and fungal, were recruited after the addition of biostimulants, which led to the support of soil C mineralization (Castiglione et al. 2021). These selected taxa were also identified as saprotrophic, endophytic, and symbiotic bacteria and fungi that have the capacity to decompose recalcitrant C sources (such as chitin and lignocellulosic material), boost fungalbacterial symbiosis and plant mycorrhization, and fulfill a plant growth-promoting (PGP) role (Aeron et al. 2021;Igiehon and Babalola 2017;Müller et al. 2020;Simmons et al. 2014). Many studies have correlated the increase in biomass, diversity, and functionality of soil fungi with a greater C and nitrogen (N) ratio (C/N), higher C efficiency, and enhanced C accumulation in soil, resulting in higher C sequestration (Malik et al. 2016;Six et al. 2006). ...
In the last decade, the exponential increase in the number of biostimulants released onto the market has raised the researcher’s curiosity to study and evaluate these alternative products. The variability in the efficiency of these products after application requires a better understanding of their modes of action. For this purpose, it is necessary to define and validate indicators that can provide information on these products' effects in improving nutrient availability, nutrient use efficiency, and plant/microorganisms' interactions. In our work, we present a scientific assessment process of different commercial prebiotics that have been seen to cause positive effects on soil and crops when applied in agricultural fields. Multispectral analyses were performed at two harvesting dates after the products’ application on soil mixed with organic wheat straws and cultivated with Zea mays L. in comparison to untreated soil. In this context, we monitored plant growth criteria, soil physicochemical parameters, soil organic matter (OM) evolution, and soil microbial community structure and diversity with an emphasis on indigenous microbial selection and root mycorrhization. This set of indicators presented a relevant tool to study the short- and medium-term effects of prebiotics on soil fertility and microbial community and their repercussions on plant growth and carbon storage. So, our experimental design is a good example of how to study the prebiotics’ functionality and evaluate their efficacity. At the end, our aim is to confirm the vital role that prebiotics will play as an innovative approach in the agroecological transition.
... Specific members of these communities, especially bacterial and fungal, were recruited after the addition of biostimulants, which led to the support of soil C mineralization (Castiglione et al. 2021). These selected taxa were also identified as saprotrophic, endophytic, and symbiotic bacteria and fungi that have the capacity to decompose recalcitrant C sources (such as chitin and lignocellulosic material), boost fungalbacterial symbiosis and plant mycorrhization, and fulfill a plant growth-promoting (PGP) role (Aeron et al. 2021;Igiehon and Babalola 2017;Müller et al. 2020;Simmons et al. 2014). Many studies have correlated the increase in biomass, diversity, and functionality of soil fungi with a greater C and nitrogen (N) ratio (C/N), higher C efficiency, and enhanced C accumulation in soil, resulting in higher C sequestration (Malik et al. 2016;Six et al. 2006). ...
Soil fertility and productivity are severely impacted by exploitation and degradation processes. These threats, coupled with population growth and climatic changes, compel us to search for innovative agroecological solutions. Prebiotics, a type of soil biostimulant, are used to enhance soil conditions and plant growth and may play a role in carbon (C) sequestration. Two commercial prebiotics, K1® and NUTRIGEO L® (referred to as SPK and SPN, respectively), were assessed for their effects on agricultural soil cultivated with Zea mays L., compared to untreated soil or control (SP). Analyses were performed at two harvesting dates: three weeks (D1) and ten weeks (D2) after the application of prebiotics. Plant growth parameters and soil characteristics were measured, focusing on soil organic matter, soil bacterial and fungal communities, and plant root mycorrhization. Regarding physicochemical parameters, both prebiotic treatments increased soil electrical conductivity, cation exchange capacity, and soluble phosphorus (P) while decreasing nitrates. Meanwhile, the SPN treatment was distinct in elevating specific cationic minerals, such as calcium (Ca) and boron (B), at D2. At the microbial level, each prebiotic induced a unique shift in the indigenous bacterial and fungal communities’ abundance and diversity, evident at D2. Simultaneously, specific microbial taxa were recruited by each prebiotic treatment, such as Caulobacter, Sphingobium, and Massilia from bacteria and Mortierella globalpina and Schizothecium carpinicola from fungi in SPK as well as Chitinophaga, Neobacillus, and Rhizomicrobium from bacteria and Sordariomycetes and Mortierella minutissima from fungi in SPN. These biomarkers were identified as (a) saprotrophs, (b) plant growth-promoting bacteria and fungi, (c) endohyphal bacteria, and (d) endophytic and symbiotic microbiota. This result was reflected in the increase in glomalin content and mycorrhization rate in the treated soils, especially by SPN. We observed that these effects led to an increase in plant biomass (shoots by 19% and 22.8% and roots by 47.8% and 35.7% dry weights for SPK and SPN, respectively) and contributed to an increase in soil C content (organic C by 8.4% and total C by 8.9%), particularly with SPN treatment. In light of these findings, the use of prebiotics ten weeks after application not only increased plant growth by improving soil characteristics and shaping its native microbial community but also demonstrated the potential to enhance C sequestration.
... Specific members of these communities, especially bacterial and fungal, were recruited after the addition of biostimulants, which led to the support of soil C mineralization (Castiglione et al. 2021). These selected taxa were also identified as saprotrophic, endophytic, and symbiotic bacteria and fungi that have the capacity to decompose recalcitrant C sources (such as chitin and lignocellulosic material), boost fungalbacterial symbiosis and plant mycorrhization, and fulfill a plant growth-promoting (PGP) role (Aeron et al. 2021;Igiehon and Babalola 2017;Müller et al. 2020;Simmons et al. 2014). Many studies have correlated the increase in biomass, diversity, and functionality of soil fungi with a greater C and nitrogen (N) ratio (C/N), higher C efficiency, and enhanced C accumulation in soil, resulting in higher C sequestration (Malik et al. 2016;Six et al. 2006). ...
Soil fertility and productivity are severely impacted by exploitation and degradation processes. These threats, coupled with population growth and climatic changes, force us to search for innovative agroecological solutions. Prebiotics are one type of soil biostimulants that are used to enhance soil conditions, plant growth, and could contribute to improve carbon sequestration. In this context, our study was designed to evaluate and explain the effects of two commercial prebiotics (K1® and NUTRIGEO L®) applied on agricultural soil mixed with organic wheat straws and cultivated with Zea mays L. in comparison to the same planted soil but untreated (control). Analysis were performed at two harvesting dates after the prebiotics’ application (3 weeks D1 and 10 weeks D2). For that, we monitored plant growth criteria, soil physico-chemical parameters, soil organic matter (OM) evolution, and soil microbial community structure and diversity with emphases on indigenous microbial selection and root mycorrhization. The obtained results demonstrated the short- and medium-term positive effects of prebiotics on soil fertility and microbial community and their repercussions on plant biomass and carbon storage. Our aim is to confirm the vital role prebiotics will play as a new alternative approach in the agroecological transition toward modern, durable, and sustainable agriculture.
... An interesting abundance of CAZymes was also found in MAGs belonging to Actinobacteria, Balneolaeota, and Deinococcus-Thermus. Identification of CAZymes from Proteobacteria, Bacteroidetes, and Actinobacteria has been also reported in several composting samples such as those based on apple pomace (Zhou et al. 2017); on leaf and wood chip compost enriched in wheat straw, poplar, and Miscanthus (Heiss-Blanquet et al. 2016); and on shredded tree branches, leaves, grass, manure, beddings, and zoo animals' food residues (Antunes et al. 2016). Actinomycetales appear to be common in the thermophilic and mature stages of the composting process, and CDSs annotated as lignocellulolytic enzymes belonging to this order have been reported before (Simmons et al. 2014;Antunes et al. 2016;Wang et al. 2016). Accordingly, a metatranscriptomic study on compost-derived microbial communities enriched on rice straw performed under thermophilic and mesophilic conditions revealed that lignocellulose-degrading enzymes mostly belonged to Proteobacteria and Bacteroidetes in the mesophilic microbial community, while the thermophilic was dominated by Actinobacteria (Simmons et al. 2014). ...
... Actinomycetales appear to be common in the thermophilic and mature stages of the composting process, and CDSs annotated as lignocellulolytic enzymes belonging to this order have been reported before (Simmons et al. 2014;Antunes et al. 2016;Wang et al. 2016). Accordingly, a metatranscriptomic study on compost-derived microbial communities enriched on rice straw performed under thermophilic and mesophilic conditions revealed that lignocellulose-degrading enzymes mostly belonged to Proteobacteria and Bacteroidetes in the mesophilic microbial community, while the thermophilic was dominated by Actinobacteria (Simmons et al. 2014). Interestingly, members of Proteobacteria have also been found in samples retrieved in the end of the composting process, including Enterobacteriales and Pseudomonadales, contributing to the degradation of the remaining biomass (Antunes et al. 2016). ...
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples’ microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples.
Key points
• Sequence- and function-based metagenomics were used to find CAZymes in compost samples.
• Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes.
• Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
... Previous researchers found the β-glucosidases from GH 1 were able to tolerate glucose concentrations ranging from several hundred to one thousand millimoles (Souza, et al., 2013;Chan, et al., 2016;Matsuzawa, et al., 2016). The abundance of the GH 1 gene encoding β-glucosidase showed an increasing trend, peaked in the thermophilic stage and then decreased during the composting of rice straw (Simmons et al., 2014). Meng et al. (2021) observed similar phenomena in the composting of bagasse pith and cow dung. ...
Vermicomposting is a promising method for corn stover management to achieve bioresource recovery and environmental protection. Most β-glucosidases, which limit the cellulose degradation rate during vermicomposting of corn stover, belong to glycoside hydrolase family 1 (GH1). This study was conducted with different earthworm densities to quantify the GH1 gene abundance and investigate the evolution of GH1 cellulase-producing microbial communities using qPCR and pyrosequencing. The results showed that β-glucosidase activity, GH1 gene abundance, TOC, and microbial communities carrying the GH1 gene were affected by processing time and earthworm density. After introducing earthworms, β-glucosidase activity increased to 1.90–2.13 U/g from 0.54 U/g. The GH1 gene abundance of treatments with earthworms (5.82E+09–6.70E+09 copies/g) was significantly higher than that of treatments without earthworms (2.48E+09 copies/g) on Day 45. Earthworms increased the richness of microbial communities. The relative abundances of Sphingobium and Dyadobacter, which are dominant genera harboring the GH1 gene, were increased by earthworms to peak values of 23.90% and 11.20%, respectively. Correlation analysis showed that Sphingobium, Dyadobacter, Trichoderma, and Starkeya were positively associated with β-glucosidases. This work sheds new light on the mechanism of cellulose degradation during vermicomposting at the molecular level.
... Conversely, the activity of the enzyme β-glucosidase was higher in the mesophilic zone, with approximately 29%, in contrast to the thermophilic zone ( Figure 3B). This can be explained by the lower transcriptional efficiency and β-glucosidase gene abundance mainly of fungi in thermophilic habitats, where more of the bacterial GH family 1 (thermophilic) is found [24]. ...
The accumulation of sewage sludge is a severe problem in many countries. Its utilization through composting has the potential to become a widely applied technology. From this perspective, our study investigated the diversity of fungi in mesophilic and thermophilic habitats when composting biosolids, cow manure, and wheat straw. It was conducted using a metagenomic approach and next-generation Illumina HiSeq2000 sequencing to reveal the fungal diversity. We found significantly enhanced microbial activity in the thermophilic phase. In contrast, the activity of enzyme β-glucosidase was 29% higher in the mesophilic zone. The range of α-diversity values were more pronounced in the mesophilic habitats than in the thermophilic ones. At the class level, the mesophilic fungi were represented by Sordariomycetes—58.7%, Pezizomycetes—15.1%, and Agaricomycetes—12.3%, while the most abundant thermophilic fungi found were Sordariomycetes—39.5%, and Pezizomycetes—9.8%. In the further clarification of genera diversity, it is striking that, at 37.2 °C, Psathyrella was the most abundant, with 35.91%, followed by Chaetomidium, with 20.11%. Among the thermophiles, Thielavia and Mortierella were the most common. Further research on microbial diversity changes over time is needed to manage the metabolic processes in obtaining quality soil amendment.
... Even though previous studies [18][19][20] have reported the expression of a plethora of genes encoding CAZy families in microbial consortia under different conditions, the focus was mainly on the bacterial members within the consortia. Our previous work [4] described the expression profile of CAZy families in interkingdom consortia with a focus on the fungal member. ...
Background
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
Results
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
Conclusions
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
... However, at the transcript level, except for CK at T2 phase, the expression of β-glucosidase genes from the GH1 family in all treatments was higher than the GH3 family. This result corroborated the observation of Simmons [36] that GH1 and GH3 family genes associated with lignocellulolytic activity overexpressed in thermophilic and mesophilic communities, respectively. Moreover, the expression of β-glucosidase genes in C L was higher, while it was lower in G H C H compared with other treatments. ...
Background
β-Glucosidase is the rate-limiting enzyme of cellulose degradation. It has been stipulated and established that β-glucosidase-producing microbial communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes. However, it is still unknown if this differential expression of functional microbial community happens accidentally or as a general regulatory mechanism, and of what biological significance it has. To investigate the composition and function of microbial communities and how they respond to different carbon metabolism pressures and the transcriptional regulation of functional genes, the different carbon metabolism pressure was constructed by setting up the static chamber during composting.
Results
The composition and function of functional microbial communities demonstrated different behaviors under the carbon metabolism pressure. Functional microbial community up-regulated glucose tolerant β-glucosidase genes expression to maintain the carbon metabolism rate by enhancing the transglycosylation activity of β-glucosidase to compensate for the decrease of hydrolysis activity under carbon catabolite repression (CCR). Micrococcales play a vital role in the resistance of functional microbial community under CCR. The transcription regulation of GH1 family β-glucosidase genes from Proteobacteria showed more obvious inhibition than other phyla under CCR.
Conclusion
Microbial functional communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes under CCR, which is a general regulatory mechanism, not accidental. Furthermore, the differentially expressed β-glucosidase gene exhibited species characteristics at the phylogenetic level.
... Overexpressed the enzyme from GH family 48, CBM family 2 and 33 domain. This overexpression in thermophilic microbial group derived from small amount of genes, presently absent in protein sequence databases (Simmons et al., 2014). Another metatranscriptomic analysis from cow rumen representing gene encoding ...
Coral reefs, an oasis of the marine ecosystem, harbour millions of microorganisms. They are among the most diverse and productive, yet one of the most threatened ecosystems on the earth. Ideally, coral reefs are considered as “rain forests of the sea” because they have a comparable primary production rate with rain forests. Although they represent approximately less than 0.1% of the total ocean surface and host nearly 25% of marine species, corals are known to rely on diverse free-living and associated microbial consortiums to drive the recycling of nutrients and support the sustainability of marine life. In addition, microbial diversity maintains the holobiont health and resilience of ecosystems in tremendous environmental stress, such as anthropogenic disturbances. Consequently, restoration and introduction of microbial diversity in the ocean are of utmost importance in order to effectively conserve and build coral reefs. Recently, significant studies have been made on the profiling of associated diverse microbial consortia. This chapter presents an overview of microbial diversity hotspots in marine corals.
... Especially given the subtlety of interindividual strain diversity, it might be impossible to determine a patient's microbial response to treatment from a taxonomic profile, but monitoring a metatranscriptome could directly measure, e.g., drug metabolism (248). Biofuel production and bioremediation are likewise highly regulation-dependent processes in free-living communities, in which MTX has been preliminarily combined with synthetic biology to engineer desired, sustainable reactions (10,26). Just as microarrays opened up entirely new avenues in molecular biology, the same remains true for community MTX: There are literally millions of genes out there whose basic intra-and intermicrobial regulatory circuits remain to be understood. ...
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In the second half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe–microbe and host–microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
