Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Abstract

Summary Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable‐isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the 13C‐DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non‐culturable microorganisms by combining both SIP and metagenome binning.

In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting

“…Functional and metabolic annotation of single-cell genomes and metagenomes allowed us to infer physiological or ecological roles for species in a complex community, which could be used to capture specific targeted as-yet-uncultured microbes from complex communities into pure cultures. , Accordingly, the genetic and metabolic characteristics of an active degrader identified by RACS-SIP can be used to elucidate its preferred cultivation conditions. Several genes involved in the metabolism of cofactors and vitamins, amino acids, and organic compounds, as well as genes associated with trace metals and aminoglycoside antibiotic resistance, were detected in the genome-SC of the active degrader Pigmentiphaga sp.…”

“…Various cultivation-independent methods have been developed to discover and explore functional, yet uncultivable microbes in the natural environment, especially their unique ecological functions and metabolic pathways. Among them, stable-isotope probing (SIP) is a powerful approach that is used to identify the functional-yet-uncultivable microbes responsible for biodegradation and assimilation of organic pollutants [e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs)] in complex microbial communities, − linking their identities to functions without the requirement of cultivation. , Nevertheless, SIP coupling with traditional molecular means such as TRFLP, high-throughput sequencing, and metagenomics can only identify the active microbes involved in biodegradation and assimilation of organic pollutants at the community level, not able to designate functional genes to their genotypes at the single-cell level , or isolate and cultivate them. − Thus, researchers are still unable to obtain the living bacterial cells responsible for in situ degradation of organic pollutants to explore their genetic and metabolic information further. Consequently, new techniques are urgently needed to improve studies at the single-cell level.…”

Redox properties of nano-sized biochar derived from wheat straw biochar

“…As suggested by Li et al, the redox properties of BC could be determined comprehensively by a variety of factors. [43][44][45]…”

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

“…Additionally, while metagenomics can reveal the composition and potential of microbial communities without traditional laboratory culture, direct evidence of microorganisms' in situ functions remains elusive (Ufarté et al., 2015). Metagenomics, coupled with SIP, offers the potential to predict the metabolism of functional microorganisms in heavy isotope‐labeled DNA and obtain comprehensive genome information for analysis of metabolic and genetic details (Cai et al., 2021; Thomas et al., 2019). Current SIP research on oil‐contaminated soil primarily focuses on specific PAH compounds like naphthalene or phenanthrene (Bao et al., 2022; Leewis et al., 2016).…”