Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter

Abstract

Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.

Rhodoferax lithotrophicus sp. nov., a neutrophilic iron-oxidizing and -reducing bacterium isolated from iron-rich freshwater sediments

“…Strain MIZ03 T grew chemoorganotrophically in R2A broth under the air and microaerobic conditions, as reported previously [15]. In the present study, we tested aerobic growth using 12 Strain MIZ03 T grew in R2A broth under anaerobic conditions (N 2 in the headspace) [15]. In this study, we tested the fermentative growth using four sugars (d-fructose, d-galactose, d-glucose, and sucrose) and two organic acids (l-lactate and pyruvate) as sole energy sources (final 10 mM for each) in liquid MWMM, instead of R2A broth, under anaerobic conditions (N 2 in the headspace).…”

“…R. ferrireducens can grow anaerobically by Fe(III) reduction. Members of the genus Rhodoferax have been reported from a wide range of natural environments, including oxic and anoxic ones, suggesting that they play a role in energy flow and biogeochemical cycle of carbon and iron [12][13][14].…”

Composition and Diversity of the Endobacteria and Ectobacteria of the Invasive Bark Beetle Hylurgus ligniperda (Fabricius) (Curculionidae: Scolytinae) in Newly Colonized Areas

“…However, Gordonia isolated from the gut of Periplaneta americana (Linnaeus) (Blattodea: Blattidae: Blattinae) showed broad-spectrum antibacterial activity [82]. Notably, Gordonia, Pseu-domonas, Acinetobacter, Sphingomonas, and Massilia were all reported to have a strong ability to biodegrade [41,[83][84][85][86][87][88], while in endobacteria, Rhodococcus, Diaphorobacter, unclassified Propionibacteriaceae, Propioniciclava, Azospira, and Paracoccus were abundant. Rhodococcus of the phylum Actinobacteriota also have a high abundance in the gut of D. valens and they have been shown to be involved in the production of the pheromone verbenone [89].…”