Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis

Characterization and Optimization of Cellulose-Degrading Bacteria Isolated from Fecal Samples of Elaphurus davidianus Through Response Surface Methodology

The screening of cellulose-degrading microorganisms from herbivores and the optimization of fermentation conditions are of great significance for the utilization of cellulose resources. In this study, we initially employed a metagenomic analysis to investigate the fecal microbiota of both captive and semi-free-ranging Père David's deer (Elaphurus davidianus) under varying environmental conditions. Subsequently, we isolated and cultured cellulase-degrading microorganisms from the fecal samples using Congo red medium. There was consistency in the dominant phyla and genera of gut microorganisms between the two groups, with only differences in abundance. Then, a cellulose-degrading strain identified as Bacillus pumilus XM was isolated after a morphological analysis and molecular identification by 16S rRNA amplicon. In addition, a series of single factor experiments and response surface analysis were conducted to determine the optimal conditions for best cellulase activity. The optimum temperature, culture time, and shaking speed for the reaction of cellulase produced by the strain Bacillus pumilus XM were 34 °C, 28 h, and 154 r/min, respectively. Under these conditions, the cellulase activity reached a maximum of 10.96 U/mL, which was relatively close to the predicted value of 10.975 U/mL. The results have enriched the existing bacterial resources and laid a foundation for the development of new enzymes, providing a theoretical basis for the rational utilization of cellulase from wild animal resources.

Quality traits drive the enrichment of Massilia in the rhizosphere to improve soybean oil content

BACKGROUND

Soybean seeds are rich in protein and oil. The selection of varieties that produce high-quality seeds has been one of the priorities of soybean breeding programs. However, the influence of improved seed quality on the rhizosphere microbiota and whether the microbiota is involved in determining seed quality are still unclear. Here, we analyzed the structures of the rhizospheric bacterial communities of 100 soybean varieties, including 53 landraces and 47 modern cultivars, and evaluated the interactions between seed quality traits and rhizospheric bacteria.

RESULTS

We found that rhizospheric bacterial structures differed between landraces and cultivars and that this difference was directly related to their oil content. Seven bacterial families (Sphingomonadaceae, Gemmatimonadaceae, Nocardioidaceae, Xanthobacteraceae, Chitinophagaceae, Oxalobacteraceae, and Streptomycetaceae) were obviously enriched in the rhizospheres of the high-oil cultivars. Among them, Oxalobacteraceae (Massilia) was assembled specifically by the root exudates of high-oil cultivars and was associated with the phenolic acids and flavonoids in plant phenylpropanoid biosynthetic pathways. Furthermore, we showed that Massilia affected auxin signaling or interfered with active oxygen-related metabolism. In addition, Massilia activated glycolysis pathway, thereby promoting seed oil accumulation.

CONCLUSIONS

These results provide a solid theoretical basis for the breeding of revolutionary soybean cultivars with desired seed quality and optimal microbiomes and the development of new cultivation strategies for increasing the oil content of seeds. Video Abstract.

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum

Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.

Microbial activity, community composition and degraders in the glyphosate-spiked soil are driven by glycine formation

Widely-used glyphosate may produce aminomethylphosphonic acid (AMPA), glycine and sarcosine. To date, little is known about effects of these degradation products on soil microorganisms and their potential degraders. Here, we incubated a soil spiked either with 2-13C-glyphosate, 13C-AMPA, 13C3-sarcosine or 13C2-glycine for 75 days. Respiration (CO2 tot) and mineralization rates of the compound (13CO2) were estimated in addition to phospholipid fatty acids (PLFAstot and 13C-PLFAs) as biomarkers to identify four groups of microorganisms (Gram-negative & Gram-positive bacteria, actinobacteria, fungi). 16S/ITS rRNA amplicon sequencing was also conducted to identify the microbial community at the phylum and genus level. The CO2 tot and 13CO2 rates were highest on day 2 in all treatments, as follows: glycine (CO2 tot: 1.09 μmol g-1; 13CO2: 18 %) > sarcosine (CO2 tot: 0.89 μmol g-1; 13CO2: 8.5 %) > glyphosate (CO2 tot: 0.67 μmol g-1; 13CO2: 2.2 %) > AMPA (CO2 tot: 0.53 μmol g-1; 13CO2: 0.3 %). Both the PLFAstot and 13C-PLFAs were highest in glycine (PLFAstot: 0.054-0.047 μmol g-1; 13C-PLFAs: 0.2-0.4 %) and glyphosate (PLFAstot: 0.049-0.047 μmol g-1; 13C-PLFAs: 0.1-0.3 %) treatments compared to sarcosine and AMPA treatments. Gram negative bacteria were major microbial group of soil microbiome as well as primary degraders of all compounds. In contrast, Gram-positive bacteria, actinobacteria and fungi could have been consumers of primary degraders. Certain genera e.g. Gemmatimonas, Arenimonas and Massilia showed increased abundance in certain treatments indicating their potential involvement in biodegradation. Based on similar time-dependent microbial activity and shifts in abundances of (13C-)PLFAs and 16S rRNA genera, we deduced that glyphosate was mainly degraded to glycine, and presumably at elevated amounts. We reported for the first time that the glycine presumably altered microbial activity and community composition rather than glyphosate directly. Future studies should thus also consider the potential impacts of degradation products of the parent compound on soil microbiomes.

Bioplastic (poly-3-hydroxybutyrate)-producing Massilia endophytica sp. nov., isolated from Cannabis sativa L. 'Cheungsam'

A rod-shaped, motile, Gram-negative bacterial strain named DM-R-R2A-13T was isolated from the plant Cannabis sativa L. 'Cheungsam'. The phylogenetic analysis of the 16S rRNA gene sequence revealed that strain DM-R-R2A-13T belongs to the family Oxalobacteraceae and is closely related to members of the genus Massilia, with Massilia flava (97.58% sequence similarity) and Massilia armeniaca (97.37% sequence similarity) being the closest members. The digital DNA-DNA hybridization (dDDH) values between strain DM-R-R2A-13T and Massilia flava CGMCC 1.10685T and Massilia armeniaca ZMN-3Twere 22.2% and 23.3%, while the average nucleotide identity (ANI) values were 78.85% and 79.63%, respectively. The DNA G+C content was measured to be 64.6 mol%. Moreover, the bacterium was found to contain polyhydroxyalkanoate (PHA) granules based on transmission electron microscopy, indicating its potential to produce bioplastic. Genome annotation revealed the presence of PHA synthase genes (phaC, phaR, phaP, and phaZ), and the biopolymer was identified as poly-3-hydroxybutyrate (PHB) based on nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) analyses. Using maltose as a carbon source, the strain produced PHB of up to 58.06% of its dry cell weight. Based on the phenotypic, chemotaxonomic, and phylogenetic characteristics, it has been determined that DM-R-R2A-13T represents a novel species belonging to the genus Massilia. As such, the name Massilia endophytica sp. nov. is proposed for this newly identified species. The type strain is DM-R-R2A-13T (= KCTC 92072T = GDMCC 1.2920T).

Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil

Crop straw contains huge amounts of exploitable energy, and efficient biomass degradation measures have attracted worldwide attention. Mining strains with high yields of cellulose-degrading enzymes is of great significance for developing clean energy and industrial production of related enzymes. In this study, we reported a high-quality genome sequence of Bacillus velezensis SSF6 strain using high-throughput sequencing technology (Illumina PE150 and PacBio) and assessed its lignocellulose degradation potential. The results demonstrated that the genome of B. velezensis SSF6 was 3.89 Mb and contained 4,015 genes, of which 2,972, 3,831 and 158 genes were annotated in the COGs (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes) and CAZyme (Carbohydrate-Active enZymes) databases, respectively, and contained a large number of genes related to carbohydrate metabolism. Furthermore, B. velezensis SSF6 has a high cellulose degradation capacity, with a filter paper assay (FPA) and an exoglucanase activity of 64.48 ± 0.28 and 78.59 ± 0.42 U/mL, respectively. Comparative genomic analysis depicted that B. velezensis SSF6 was richer in carbohydrate hydrolase gene. In conclusion, the cellulose-degrading ability of B. velezensis SSF6 was revealed by genome sequencing and the determination of cellulase activity, which laid a foundation for further cellulose degradation and bioconversion.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov

Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

Massilia phyllostachyos sp. nov., Isolated from the Roots of Moso Bamboo in China

A Gram-negative, strictly aerobic, motile, and rod-shaped bacterial strain G4R7^T was isolated from the roots of moso bamboo (Phyllostachys edulis) in Zhejiang, Hangzhou Province, China. After comparing 16S rRNA gene sequences, strain G4R7^T exhibited the highest similarities with Massilia neuiana PTW21^T (98.3%), followed by M. agri K-3-1^T (98.3%), M. consociate CCUG 58010^T (97.7%), M. niastensis 5516S-1^T (97.7%) and M. yuzhufengensis ZD1-4^T (97.6%). The phylogenetic analysis revealed that strain G4R7^T belonged to the genus Massilia. The draft genome of strain G4R7^T was 5.81 Mb, and the G+C content was 64.4%. The average nucleotide identity values between G4R7^T and another related member of the genus Massilia ranged from 76.6 to 87.2%, and the digital DNA-DNA hybridization ranged from 20.7 to 27.9%. Strain G4R7^T grew at 15-37 °C (optimum 25-30 °C) and pH 6.0-9.0 (optimum pH 7.0) in the presence of 0-3% (w/v) NaCl (optimum 0%). The respiratory quinone was Q-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and aminophospholipid. The major cellular fatty acids were C_10:0 3OH, C_12:0, C_12:0 2OH, and C_16:0, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c). As per the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain G4R7^T represents a new species of genus Massilia, for which the name Massilia phyllostachyos sp. nov. is proposed. The type strain is G4R7^T (=ACCC 61911^T=GDMCC 1.2961^T=JCM 35225^T).