András Táncsics

The gut microbiota plays a central role in poultry health and production performance, yet its response to intensive fattening protocols and postbiotic supplementation in geese remains poorly characterized. This study used 16S rRNA gene amplicon sequencing to profile ileal and caecal microbial communities from geese raised under two fattening protocols, with or without postbiotic supplementation, and assessed the effect of 24 h post-mortem chilling on apparent community composition. Fattening protocol was associated with the largest differences in gut microbial structure, producing significant shifts in beta diversity in both the ileum and the caecum (although protocol, age at slaughter, and duration of postbiotic exposure co-varied between cohorts and cannot be fully disentangled), accompanied by extensive taxon-level differences identified by LEfSe. Postbiotic supplementation did not significantly alter overall community structure under force-feeding conditions but produced a taxon-specific, trend-level shift in the caecum under restricted feeding, suggesting that its effect depends on the continuity of supplementation relative to slaughter. Alpha diversity did not differ significantly in the ileum, but caecal richness differed significantly between the G2 and G5 postbiotic-supplemented groups (Conover–Iman test, adjusted p < 0.05). The warm- and chilled-dissection groups differed in ileal but not caecal community composition (individual-animal variation cannot be separated from the effect of chilling in this comparison, as the two groups consisted of different birds), indicating that dissection timing is an important methodological variable in goose microbiome research. These findings highlight cohort- and protocol-related differences as key correlates of gut microbial composition in geese and provide a framework for optimizing postbiotic supplementation strategies and sampling standardization in waterfowl production.

Rhodococcus erythropolis NI86/21, isolated from maize rhizosphere in Hungary, possesses one of the largest genomes (8.046 Mb) within the species. The genome comprises a 6.83 Mb chromosome and 1.22 Mb of extrachromosomal elements, including three circular and two fragmented linear plasmids. Comparative analysis identified five horizontally acquired genomic islands (HGTi), totaling 0.64 Mb with mosaic-like architecture derived from plasmids, phages, and chromosomal segments of other Nocardiaceae . Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis revealed a lower expression of genes located in HGT elements (53%) compared to core chromosomal genes (73%), indicating regulatory silencing of foreign DNA. Nevertheless, an inducible cytochrome P450 monooxygenase (CYP116) responsible for thiocarbamate and atrazine degradation is encoded on HGTi_V and actively expressed upon herbicide exposure. Strikingly, an identical CYP450 locus is present on a conjugative plasmid in Rhodococcus sp. TE1 isolated from thiocarbamate-treated soil in Canada, demonstrating independent acquisition of the same catabolic module from a high GC% content Rhodococcus , under similar selective pressure. Frequent recombination between chromosomal and mobile elements generates the observed mosaic-like HGT structures, which we found common for R. erythropolis strains. These results highlight extraordinary genomic plasticity and rapid adaptive evolution in Rhodococci , enabling efficient colonization of herbicide-contaminated agro-ecosystems. IMPORTANCE: Rhodococcus erythropolis NI86/21 exemplifies how bacterial genomes evolve through horizontal gene transfer and mobile elements. Its unusually large, plastic genome contains extensive HGT islands and a high load of active transposons, which shape mosaic genomic architectures and hinder complete genome assembly. These horizontally acquired regions, although partially silenced, encode key adaptive functions such as an inducible CYP116 monooxygenase enabling thiocarbamate and atrazine degradation. Remarkably, an identical CYP116 module is present in Rhodococcus sp. TE1 from thiocarbamate-treated Canadian soil, demonstrating that similar environmental pressures can drive independent acquisition of the same biodegradation trait. Together, the dynamic transposon activity, mosaic HGT structure, and geographically convergent gene recruitment highlight the extraordinary genomic plasticity of R. erythropolis and underscore its rapid adaptive potential in agro-ecosystems, with implications for microbial evolution and bioremediation strategies.

A novel carbon monoxide (CO)-oxidizing bacterial strain designated as SB112 ^T was enriched and isolated from Ilex aquifolium leaves from Tocil Wood Nature Reserve in Coventry, UK. The strain was Gram reaction-negative, aerobic, rod-shaped, motile with a polar flagellum and non-spore-forming. Growth of strain SB112 ^T was observed at 10–45 °C, pH 6.0–12.0 and NaCl concentrations of 1–3%. The genomic DNA G+C content was 58.3 mol%, and the major fatty acids (>10%) of strain SB112 ^T were C _18 : 1 ω7c, C _18 : 1 ω7c 11-methyl and C _19 : 0 cyclo ω7c. Major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and a phospholipid. Strain SB112ᵀ contains ubiquinone-10 as the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SB112 ^T formed a separate lineage within the family Phyllobacteriaceae , showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives Aminobacter niigataensis , Aminobacter aminovorans and Mesorhizobium plurifarium , respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family Phyllobacteriaceae . However, its phylogenetic position did not correspond to any known genus within this family. The genome of strain SB112 ^T was found to possess the form II coxL gene, which encodes the large subunit of the CO dehydrogenase and potentially enables CO oxidation. The average nucleotide identity and digital DNA–DNA hybridization with members of closely related genera yielded values below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Based on the phenotypic, chemotaxonomic, phylogenetic, genomic and physiological properties, strain SB112 ^T is considered to represent a novel species of a new genus Foliimonas within the family Phyllobacteriaceae for which the name Foliimonas ilicis gen. nov., sp. nov. is proposed. The type of strain is SB112 ^T (=LMG 33802 ^T , =NCAIM B.02691 ^T ).

A Gram-stain-negative strain, designated as Zidic-5^T, was isolated from diclofenac-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain Zidic-5^T belongs to the genus Labrys, with the highest 16S rRNA gene similarity to Labrys neptuniae LMG 23578^T (99.13%), followed by Labrys portucalensis F11^T (99.06%), Labrys methylaminiphilus JLW10^T (98.58%) and Labrys okinawensis DSM 18385^T (98.32%). The draft genome sequence of strain Zidic-5^T is 7.64 Mb long, and the G+C content of the genome is 63.5 mol%. The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain Zidic-5^T and its closest relatives were below the threshold values for species demarcation, confirming that strain Zidic-5^T is distinctly separated from its closest relatives. Additionally, comparative whole-genome analysis of type strains of L. neptuniae and L. portucalensis indicated that they belong to the same genomic species, suggesting that L. portucalensis is a later heterotypic synonym of L. neptuniae. Cells of strain Zidic-5^T were strictly aerobic, coccoid-shaped and non-motile. The predominant fatty acids (>10% of the total) of strain Zidic-5^T were C_18 : 1 ω7c, C_16 : 0 and C_19 : 0 cyclo ω7c. The major ubiquinone of strain Zidic-5^T was Q-10, while the major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on the polyphasic study, it is concluded that strain Zidic-5^T represents a novel species of the genus Labrys; thus, the name of Labrys sedimenti sp. nov. is proposed. The type strain of the species is strain Zidic-5^T (=LMG 33565^T=NCAIM B.02686^T).

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and ¹³C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of “heavy” and “light” DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.

Salinization and sodification are serious and worldwide growing threats to healthy soil functions. Although plants developed a plethora of traits to cope with high salinity, soil bacteria are also essential players of the adaptation process. However, there is still lack of knowledge on how other biotic and abiotic factors, such as land use or different soil properties, affect the bacterial community structure of these soils. Therefore, besides soil chemical and physical investigations, bacterial communities of differently managed salt-affected soils were analysed through 16S rRNA gene Illumina amplicon sequencing and compared. Results have shown that land use and soil texture were the main drivers in shaping the bacterial community structure of the Hungarian salt-affected soils. It was observed that at undisturbed pasture and meadow sites, soil texture and the ratio of vegetation cover were the determinative factors shaping the bacterial community structures, mainly at the level of phylum Acidobacteriota. Sandy soil texture promoted the high abundance of members of the class Blastocatellia, while at the slightly disturbed meadow soil showing high clay content was dominated by members of the class Acidobacteriia. The OTUs belonging to the class Ktedonobacteria, which were reported mostly in geothermal sediments, reached a relatively high abundance in the meadow soil.

A Gram-stain-negative strain, designated as D2M1^T was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1^T belongs to the genus Acidovorax , with the highest 16S rRNA gene similarity to Acidovorax delafieldii DSM 64^T (99.93 %), followed by Acidovorax radicis DSM 23535^T (98.77 %) and Acidovorax kalamii MTCC 12652^T (98.76 %). The draft genome sequence of strain D2M1^T is 5.49 Mb long, and the G+C content of the genome is 64.2 mol%. Orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain D2M1^T and its closest relatives were below the threshold values for species demarcation confirming that strain D2M1^T is distinctly separated from its closest relatives. The whole genome analysis of the strain revealed a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including an I.2.C-type catechol 2,3-dioxygenase (C23O) gene. The strain was able to degrade benzene and ethylbenzene as sole sources of carbon and energy under aerobic and microaerobic conditions. Cells were facultatively aerobic rods and motile with a single polar flagellum. The predominant fatty acids (>10 % of the total) of strain D2M1^T were summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c), C_16 : 0 and summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c). The major ubiquinone of strain D2M1^T was Q8, while the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on polyphasic data, it is concluded that strain D2M1^T represents a novel species of the genus Acidovorax , for which the name of Acidovorax benzenivorans sp. nov. is proposed. The type strain of the species is strain D2M1^T (=DSM 115238^T=NCAIM B.02679^T).

Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and xylene (BTEX) are the most common contaminants of the groundwater and can easily contaminate drinking water sources due to their relatively high water solubility. Among these compounds, benzene is known to have carcinogenic properties and is considered to be persistent under anoxic conditions. Although deep knowledge was acquired both on the aerobic and anaerobic degradation of benzene in the past three decades, the diversity of those bacteria which are able to degrade it under microaerobic conditions, is still unknown. To come over this limitation aerobic and microaerobic benzene-degrading microcosms were established using groundwater sediment of a BTEX-contaminated site and the evolved bacterial communities were investigated through a polyphasic approach including multiomics analysis and DNA stable isotope probing. The obtained results shed light on the fact that the aerobic and microaerobic benzene-degrading bacterial communities were distinctly different. In the aerobic microcosms members of the genus Pseudomonas overwhelmingly dominated the bacterial communities by showing even 40-50% abundance. In contrast, under microaerobic conditions members of the genera Azovibrio and Malikia dominated the communities, while the abundance of Pseudomonas drastically decreased compared to that of was observable in the aerobic microcosms. Results obtained by the analysis of microcosms spiked with ¹³C₆-benzene confirmed these observations. In heavy DNA fractions obtained from the aerobic microcosms the enrichment of Pseudomonas and Rhizobiaceae-related 16S rRNA gene fragments was observable. At the same time, labelled DNA from the microaerobic microcosms contained mostly Azovibrio and Malikia-related sequences, while the abundance of Pseudomonas 16S rRNA gene sequences was below 2%. Besides, by using metagenomic dataset of a previous microaerobic experiment we managed to reconstruct an Azovibrio genome, in which a complete meta-cleavage pathway for the aerobic degradation of aromatic hydrocarbons was identified. Overall, it can be concluded that under microaerobic conditions members of Comamonadaceae and Rhodocyclaceae can be the key benzene degraders in contaminated subsurface environments.

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.