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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.

ABSTRACT: Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2?Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and ?-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, "profiling" of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ?10?Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.

SUBMITTER: Jimenez DJ

PROVIDER: S-EPMC4561380 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.

Jiménez Diego Javier DJ Chaves-Moreno Diego D van Elsas Jan Dirk JD

Scientific reports 20150907

Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohy ...[more]

PMID: 26343383

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Project description:BackgroundMixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures.ResultsIn order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions.ConclusionIn an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.

Project description:Straw pollution and the increasing scarcity of phosphorus resources in many regions of China have had severe impacts on the growing conditions for crop plants. Using microbial methods to enhance straw decomposition rate and phosphorus utilization offers effective solutions to address these problems. In this study, a microbial consortium 6 + 1 (consisting of a straw-degrading bacterium and a phosphate-solubilizing bacterium) was formulated based on their performance in straw degradation and phosphorus solubilization. The degradation rate of straw by 6 + 1 microbial consortium reached 48.3% within 7 days (The degradation ability was 7% higher than that of single bacteria), and the phosphorus dissolution rate of insoluble phosphorus reached 117.54 mg·L- 1 (The phosphorus solubilization ability was 29.81% higher than that of single bacteria). In addition, the activity of lignocellulosic degrading enzyme system was significantly increased, the activities of endoglucanase, β-glucosidase and xylanase in the microbial consortium were significantly higher than those in the single strain (23.16%, 28.02% and 28.86%, respectively). Then the microbial consortium was processed into microbial agents and tested in rice pots. The results showed that the microbial agent significantly increased the content of organic matter, available phosphorus and available nitrogen in the soil. Ongoing research focuses on the determination of the effects and mechanisms of a functional hybrid system of straw degradation and phosphorus removal. The characteristics of the two strains are as follows: Straw-degrading bacteria can efficiently degrade straw to produce glucose-based carbon sources when only straw is used as a carbon source. Phosphate-solubilizing bacteria can efficiently use glucose as a carbon source, produce organic acids to dissolve insoluble phosphorus and consume glucose at an extremely fast rate. The analysis suggests that the microbial consortium 6 + 1 outperformed individual strains in terms of both performance and application effects. The two strains within the microbial consortium promote each other during their growth processes, resulting in a significantly higher rate of carbon source consumption compared to the individual strains in isolation. This increased demand for carbon sources within the growth system facilitates the degradation of straw by the strains. At the same time, the substantial carbon consumption during the metabolic process generated a large number of organic acids, leading to the solubilization of insoluble phosphorus. It also provides a basis for the construction of this type of microbial consortium.

Project description:BackgroundFunctional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered.ResultsHere, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0.ConclusionsThis study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.

Project description:Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

Project description:BackgroundSoil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice-wheat rotation systems.MethodsThe effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice-wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed.ResultsCompared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0-20 and 20-40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0-20 cm soil and Neurospora in macroaggregates in 20-40 cm soil); decreased pathogenic fungi (Monographella in macroaggregates and Gibberella in microaggregates in 0-20 cm soil) and CO2-emission-related fungi (Pyrenochaetopsis in microaggregates and silt clay in 0-40 cm soil) (p < 0.05). Straw and biochar with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer with biochar showing better effects than straw.

Project description:Lignin is nature's largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.

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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.

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