Pedobacter helvus sp. nov., isolated from farmland soil

Rapid screening of indigenous degrading microorganisms for enhancing in-situ bioremediation of organic pollutants-contaminated soil

Organic pollutants (OPs) have caused severe environmental contaminations in the world and aroused wide public concern. Autochthonous bioaugmentation (ABA) is considered a reliable bioremediation approach for OPs contamination. However, the rapid screening of indigenous degrading strains from in-situ environments remains a primary challenge for the practical application of ABA. In this study, 3,5,6-Trichloro-2-pyridinol (TCP, an important intermediate in the synthesis of various pesticides) was selected as the target OPs, and DNA stable isotope probing (DNA-SIP) combined with high-throughput sequencing was employed to explore the rapid screening of indigenous degrading microorganisms. The results of DNA-SIP revealed a significant enrichment of OTU557 (Cupriavidus sp.) in the 13C-TCP-labeled heavy DNA fractions, indicating that it is the key strain involved in TCP metabolism. Subsequently, an indigenous TCP degrader, Cupriavidus sp. JL-1, was rapidly isolated from native soil based on the analysis of the metabolic substrate spectrum of Cupriavidus sp. Furthermore, ABA of strain JL-1 demonstrated higher remediation efficacy and stable survival compared to the exogenous TCP-degrading strain Cupriavidus sp. P2 in in-situ TCP-contaminated soil. This study presents a successful case for the rapid acquisition of indigenous TCP-degrading microorganisms to support ABA as a promising strategy for the in-situ bioremediation of TCP-contaminated soil.

Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria

Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.

Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.

Pedobacter montanisoli sp. nov., isolated from soil

A white-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated CYS-01^T, was obtained from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 28 °C. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain CYS-01^T formed a lineage within the family Sphingobacteriaceae and clustered with members of the genus Pedobacter. The closest relatives were Pedobacter xixiisoli CGMCC 1.12803^T (95.70 % sequence similarity), Pedobacter ureilyticus THG-T11^T (95.35 %), Pedobacter helvus P-25^T (95.28 %), Pedobacter chitinilyticus CM134L-2^T (94.94 %), Pedobacter nanyangensis Q-4^T (94.73 %) and Pedobacter zeaxanthinifaciens TDMA-5^T (94.07 %). The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, unidentified lipids and an unidentified glycolipid. The predominant cellular fatty acids were iso-C_15 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and iso-C_17 : 0 3-OH. The DNA G+C content was 36.6 mol%. Based on the results of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain CYS-01^T represents novel species in the genus Pedobacter, for which the name Pedobacter montanisoli sp. nov. is proposed. The type strain is CYS-01^T (=KACC 22655^T=NBRC 115630^T).

A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[¹³C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.