Genome Assemblies of Three Soil-Associated Devosia species: D. insulae, D. limi, and D. soli

Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

To systematically explore and analyze the microbial composition and function of microbial consortium M44 with straw degradation in the process of subculture at low temperature. In this study, straw degradation characteristics of samples in different culture stages were determined. MiSeq high-throughput sequencing technology was used to analyze the evolution of community structure and its relationship with degradation characteristics of microbial consortium in different culture periods, and the PICRUSt function prediction analysis was performed. The results showed that straw degradation rate, endoglucanase activity, and filter paper enzyme activity of M44 generally decreased with increasing culture algebra. The activities of xylanase, laccase, and lignin peroxidase, as well as VFA content, showing a single-peak curve change with first an increase and then decrease. In the process of subculture, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in different culture stages. Pseudomonas, Flavobacterium, Devosia, Brevundimonas, Trichococcus, Acinetobacter, Dysgonomonas, and Rhizobium were functional bacteria in different culture stages. It was found by PICRUSt function prediction that the functions were concentrated in amino acid transport and metabolism, carbohydrate transship and metabolism related genes, which may contain a large number of fibers and lignin degrading enzyme genes. In this study, the microbial community succession and the gene function in different culture periods were clarified and provide a theoretical basis for screening and rational utilization of microbial consortia.

Deoxynivalenol Degradation by Various Microbial Communities and Its Impacts on Different Bacterial Flora

Deoxynivalenol, a mycotoxin that may present in almost all cereal products, can cause huge economic losses in the agriculture industry and seriously endanger food safety and human health. Microbial detoxifications using microbial consortia may provide a safe and effective strategy for DON mitigation. In order to study the interactions involving DON degradation and change in microbial flora, four samples from different natural niches, including a chicken stable (expJ), a sheep stable (expY), a wheat field (expT) and a horse stable (expM) were collected and reacted with purified DON. After being co-incubated at 30 °C with 130 rpm shaking for 96 h, DON was reduced by 74.5%, 43.0%, 46.7%, and 86.0% by expJ, expY, expT, and expM, respectively. After DON (0.8 mL of 100 μg/mL) was co-cultivated with 0.2 mL of the supernatant of each sample (i.e., suspensions of microbial communities) at 30 °C for 96 h, DON was reduced by 98.9%, 99.8%, 79.5%, and 78.9% in expJ, expY, expT, and expM, respectively, and was completely degraded after 8 days by all samples except of expM. DON was confirmed being transformed into de-epoxy DON (DOM-1) by the microbial community of expM. The bacterial flora of the samples was compared through 16S rDNA flux sequencing pre- and post the addition of DON. The results indicated that the diversities of bacterial flora were affected by DON. After DON treatment, the most abundant bacteria belong to Galbibacter (16.1%) and Pedobacter (8.2%) in expJ; Flavobacterium (5.9%) and Pedobacter (5.5%) in expY; f_Microscillaceae (13.5%), B1-7BS (13.4%), and RB41 (10.5%) in expT; and Acinetobacter (24.1%), Massilia (8.8%), and Arthrobacter (7.6%) in expM. This first study on the interactions between DON and natural microbial flora provides useful information and a methodology for further development of microbial consortia for mycotoxin detoxifications.

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

Bacterial Epimerization as a Route for Deoxynivalenol Detoxification: the Influence of Growth and Environmental Conditions

Deoxynivalenol (DON) is a toxic secondary metabolite produced by several Fusarium species that infest wheat and corn. Food and feed contaminated with DON pose a health risk to both humans and livestock and form a major barrier for international trade. Microbial detoxification represents an alternative approach to the physical and chemical detoxification methods of DON-contaminated grains. The present study details the characterization of a novel bacterium, Devosia mutans 17-2-E-8, that is capable of transforming DON to a non-toxic stereoisomer, 3-epi-deoxynivalenol under aerobic conditions, mild temperature (25–30°C), and neutral pH. The biotransformation takes place in the presence of rich sources of organic nitrogen and carbon without the need of DON to be the sole carbon source. The process is enzymatic in nature and endures a high detoxification capacity (3 μg DON/h/10⁸ cells). The above conditions collectively suggest the possibility of utilizing the isolated bacterium as a feed treatment to address DON contamination under empirical field conditions.

Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16

The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994 bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation.