Molecular characteristics of xenobiotic-degrading sphingomonads

Unveiling the Characteristics of Microbiota in Different Mucosal Layers of Leopard Coral Grouper (Plectropomus leopardus)

Mucosal microbiomes play an important role in digestion, nutrition, and resistance to pathogens and toxins in fish; thus, characterizing the mucosal microbiomes of economically important fish species is paramount. In this study, mucosal microbiomes of healthy leopard coral grouper (Plectropomus leopardus), which is of economic importance worldwide, were systematically analyzed and compared by using 16S rRNA amplicon sequencing. The analysis of alpha-diversity and beta-diversity revealed significant differences in the structure and composition of the microbial community between different mucosal layers of P. leopardus. The skin microbiota showed the lowest microbial diversity among the three tissues, and the highest interindividual variability within gill groups was observed. Proteobacteria is the dominant phylum of the gut, skin, and gill microbiomes. Microbial biomarkers of the three mucosal tissues were identified, with the genera Parvibaculum, Aminobacter, Sphingobium, and Ralstonia for skin; Mesoflavibacter, Winogradskyella, Malaciobacter, Nautella, and Marinobacterium for gills; and Cetobacterium, Photobacterium, and Vibrio for gut. These genera were also the core microorganisms in each tissue. A large number of identical pathways of the three mucosal surfaces microbiome (e.g., pathways related to metabolism, human diseases, genetic/environmental information processing) and some specifically enriched pathways in each tissue were identified. Co-occurrence network analysis revealed that there were more ecological communities and higher functional diversity in the gill microbiota, and the interactions between gut microbiota are closer and more stable. Our study provides a new perspective for a comprehensive understanding of the mucosal microbiota of P. leopardus, contributing to an in-depth exploration of the interaction between fish and microorganisms, and may help to predict potential disease outbreaks, thus promoting the development of the fish farming industry.

Raman Microspectroscopy to Trace the Incorporation of Deuterium from Labeled (Micro)Plastics into Microbial Cells

The ubiquitous use of plastics demands thoughtfulness about their fate in the environment. Biodegradability is, therefore, a prerequisite for the future use of plastics in many applications, including agriculture. Here, we bring forward stable isotope (resonance) Raman microspectroscopy at the single-cell level to broaden the mechanistic understanding of microbial degradation of (micro)plastics in natural systems. We selected perdeuterated d-polylactic acid (dPLA) as model plastic, synthesized from d-lactic acid-d4, via enantioselective, biocatalytic reduction of pyruvate-d3. With dPLA in hand, we traced the deuterium label during incubation experiments into microbial biomass using C-D vibrations (appear in the Raman-silent region of undeuterated biomass, 2050-2300 cm-1). The 2068 cm-1 C-D band was indicative of strongly deuterated lipids enabling the detection of metabolic differences during incubation with dPLA (i.e., stronger lipid and weaker protein deuteration) compared to glucose-d12 and D2O as alternative D sources. Single-cell analysis was the key to detecting phenotypic heterogeneity and classifying cells of the naturally occurring bacterium Sphingomonas koreensis in two clusters: one showed a significantly stronger deuteration level than the Escherichia coli control, whereas the other was nonlabeled. The deuterium label could even be detected in the strong resonance Raman signal of carotenoids, highlighting the potential for high throughput technologies like imaging and cell sorting. To further demonstrate the transferability to environmental samples, the experiment was repeated with soil bacteria isolates, and deuterium uptake from dPLA into microbial biomass was observed after 2 weeks.

UV-C Exposure Enhanced the Cd2+ Adsorption Capability of the Radiation-Resistant Strain Sphingomonas sp. M1-B02

Microbial adsorption is a cost-effective and environmentally friendly remediation method for heavy metal pollution. The adsorption mechanism of cadmium (Cd) by bacteria inhabiting extreme environments is largely unexplored. This study describes the biosorption of Cd2+ by Sphingomonas sp. M1-B02, which was isolated from the moraine on the north slope of Mount Everest and has a good potential for biosorption. The difference in Cd2+ adsorption of the strain after UV irradiation stimulation indicated that the adsorption reached 68.90% in 24 h, but the adsorption after UV irradiation increased to 80.56%. The genome of strain M1-B02 contained antioxidant genes such as mutL, recA, recO, and heavy metal repair genes such as RS14805, apaG, chrA. Hydroxyl, nitro, and etceteras bonds on the bacterial surface were involved in Cd2+ adsorption through complexation reactions. The metabolites of the strains were significantly different after 24 h of Cd2+ stress, with pyocyanin, L-proline, hypoxanthine, etc., being downregulated and presumably involved in Cd2+ biosorption and upregulated after UV-C irradiation, which may explain the increase in Cd2+ adsorption capacity of the strain after UV-C irradiation, while the strain improved the metabolism of the antioxidant metabolite carnosine, indirectly increasing the adsorption capacity of the strains for Cd2+.

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16 S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1 h in microcosms. Heating to 60 °C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100 °C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60 °C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing

Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination of environment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.

Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train

Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.

Remediation of isoproturon-contaminated soil by Sphingobium sp. strain YBL2: Bioaugmentation, detoxification and community structure

The widely used phenylurea herbicide isoproturon (IPU) and its residues can inhibit the growth of subsequently planted crops. However, reports on bioremediation of IPU-contaminated soil are scarce. In this study, Sphingobium sp. strain YBL2-gfp (a derivative of the IPU-degrading Sphingobium sp. strain YBL2 isolated by our lab) was constructed to bioremediate IPU-contaminated soil. In pot experiments, strain YBL2-gfp colonized the roots of wheat and eliminated IPU residues in the soil within 21 d, effectively alleviating its toxicity and restoring wheat growth. IPU treatment reduced the richness and diversity of soil bacteria, while inoculation YBL2-gfp mainly affected richness with less impact on diversity. The high concentrations of IPU and inoculation of YBL2-gfp alone reduced the soil microbial community connections, while bioaugmentation treatment enhanced the soil microbial community connections. Additionally, strain YBL2-gfp stimulated the metabolic capacity of the indigenous microbes, promoting the degradation of IPU and reducing the negative impact of high concentrations of IPU on microbial community. Taken together, this study offers relatively comprehensive insights into the practical application of bioaugmentation, demonstrating that strain YBL2 has the potential to remediate IPU-contaminated soils.

Sphingobium sp. SJ10-10 encodes a not-yet-reported chromate reductase and the classical Rieske dioxygenases to simultaneously degrade PAH and reduce chromate

Both polycyclic aromatic hydrocarbons (PAHs) and heavy metals persist in the environment and are toxic to organisms. Their co-occurrence makes any of them difficult to remove during bioremediation and poses challenges to environmental management and public health. Microorganisms capable of effectively degrading PAHs and detoxifying heavy metals concurrently are required to improve the bioremediation process. In this study, we isolated a new strain, Sphingobium sp. SJ10-10, from an abandoned coking plant and demonstrated its capability to simultaneously degrade 92.6 % of 75 mg/L phenanthrene and reduce 90 % of 3.5 mg/L hexavalent chromium [Cr(VI)] within 1.5 days. Strain SJ10-10 encodes Rieske non-heme iron ring-hydroxylating oxygenases (RHOs) to initiate PAH degradation. Additionally, a not-yet-reported protein referred to as Sphingobium chromate reductase (SchR), with low sequence identity to known chromate reductases, was identified to reduce Cr(VI). SchR is distributed across different genera and can be classified into two classes: one from Sphingobium members and the other from non-Sphingobium species. The widespread presence of SchR in those RHO-containing Sphingobium members suggests that they are excellent candidates for bioremediation. In summary, our study demonstrates the simultaneous removal of PAHs and Cr(VI) by strain SJ10-10 and provides valuable insights into microbial strategies for managing complex pollutant mixtures.

Multi-omics differences in the bone marrow between essential thrombocythemia and prefibrotic primary myelofibrosis

Essential thrombocythemia (ET) and prefibrotic primary myelofibrosis (pre-PMF) are Philadelphia chromosome-negative myeloproliferative neoplasms. These conditions share overlapping clinical presentations; however, their prognoses differ significantly. Current morphological diagnostic methods lack reliability in subtype differentiation, underlining the need for improved diagnostics. The aim of this study was to investigate the multi-omics alterations in bone marrow biopsies of patients with ET and pre-PMF to improve our understanding of the nuanced diagnostic characteristics of both diseases. We performed proteomic analysis with 4D direct data-independent acquisition and microbiome analysis with 2bRAD-M sequencing technology to identify differential protein and microbe levels between untreated patients with ET and pre-PMF. Laboratory and multi-omics differences were observed between ET and pre-PMF, encompassing diverse pathways, such as lipid metabolism and immune response. The pre-PMF group showed an increased neutrophil-to-lymphocyte ratio and decreased high-density lipoprotein and cholesterol levels. Protein analysis revealed significantly higher CXCR2, CXCR4, and MX1 levels in pre-PMF, while APOC3, APOA4, FABP4, C5, and CFB levels were elevated in ET, with diagnostic accuracy indicated by AUC values ranging from 0.786 to 0.881. Microbiome assessment identified increased levels of Mycobacterium, Xanthobacter, and L1I39 in pre-PMF, whereas Sphingomonas, Brevibacillus, and Pseudomonas_E were significantly decreased, with AUCs for these genera ranging from 0.833 to 0.929. Our study provides preliminary insights into the proteomic and microbiome variations in the bone marrow of patients with ET and pre-PMF, identifying specific proteins and bacterial genera that warrant further investigation as potential diagnostic indicators. These observations contribute to our evolving understanding of the multi-omics variations and possible mechanisms underlying ET and pre-PMF.

Soil bacterial community diversity and life strategy during slope restoration on an uninhabited island: changes under the aggregate spray-seeding technique

AIMS

We investigated the effects of the aggregate spray-seeding (ASS) technique on soil bacterial community diversity, life strategies, and seasonal change.

METHODS AND RESULTS

Soil from six plots with original vegetation (CK, n = 6) was compared to soil from 15 plots with spray-seeding restoration (SR, n = 15) using environmental DNA sequencing. The bacterial Shannon and Chao1 indices of SR soils were significantly greater (P < 0.05) than those of CK soils. The Chao1 index for the SR soil bacterial community was significantly greater in summer (P < 0.05) than in winter. The ratio of the relative abundance of bacterial K-strategists to r-strategists (K/r) and the DNA guanine-cytosine (GC) content in the SR soil were significantly lower (P < 0.05) than those in the CK soil. Principal coordinate analysis revealed significant differences between the SR and CK bacterial communities. The GC content was positively correlated with the K/r ratio. Soil conductivity was negatively associated with the K/r ratio and GC content, indicating that ionic nutrients were closely related to bacterial life strategies.

CONCLUSIONS

The ASS technique improved soil bacterial diversity, altered community composition, and favored bacterial r-strategists.

Revealing the biological significance of multiple metabolic pathways of chloramphenicol by Sphingobium sp. WTD-1

Chloramphenicol (CAP) is an antibiotic that commonly pollutes the environment, and microorganisms primarily drive its degradation and transformation. Although several pathways for CAP degradation have been documented in different bacteria, multiple metabolic pathways in the same strain and their potential biological significance have not been revealed. In this study, Sphingobium WTD-1, which was isolated from activated sludge, can completely degrade 100 mg/L CAP within 60 h as the sole energy source. UPLC-HRMS and HPLC analyses showed that three different pathways, including acetylation, hydroxyl oxidation, and oxidation (C1-C2 bond cleavage), are responsible for the metabolism of CAP. Importantly, acetylation and C3 hydroxyl oxidation reduced the cytotoxicity of the substrate to strain WTD-1, and the C1-C2 bond fracture of CAP generated the metabolite p-nitrobenzoic acid (PNBA) to provide energy for its growth. This indicated that the synergistic action of three metabolic pathways caused WTD-1 to be adaptable and able to degrade high concentrations of CAP in the environment. This study deepens our understanding of the microbial degradation pathway of CAP and highlights the biological significance of the synergistic metabolism of antibiotic pollutants by multiple pathways in the same strain.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

Integrated management of fruit trees and Bletilla striata: implications for soil nutrient profiles and microbial community structures

Introduction

Forest medicinal compound systems in agroforestry ecosystems represent a multi-layered cultivation approach that utilizes forest resources efficiently. However, research on how these systems affect soil nutrients and microbial communities is limited.

Methods

This study compared the soil chemical properties and microbial communities of Bletilla striata (C) grown alone versus in agroforestry systems with apple (PB), pear (LB), and peach trees (TB), aiming to understand the impact of these systems on soil health and microbial diversity.

Results

Soil in the GAB systems showed increased levels of essential nutrients but lower pH and ammonium nitrogen levels compared to the control. Significant improvements in organic matter, total phosphorus, and total potassium were observed in TB, PB, and LB systems, respectively. The bacterial diversity increased in GAB systems, with significant changes in microbial phyla indicative of a healthier soil ecosystem. The correlation between soil properties and bacterial communities was stronger than with fungal communities.

Discussion

Integrating B. striata with fruit trees enhances soil nutrients and microbial diversity but may lead to soil acidification. Adjustments such as using controlled-release fertilizers and soil amendments like lime could mitigate negative impacts, improving soil health in GAB systems.

Sphingomonas panaciterrae PB20 increases growth, photosynthetic pigments, antioxidants, and mineral nutrient contents in spinach (Spinacia oleracea L.)

Plant growth promoting rhizobacteria (PGPR) have been intensively investigated in agricultural crops for decades. Nevertheless, little information is available on the application of Sphingomonas spp. as a PGPR particularly in vegetables, despite of potential plant growth promoting traits of this group. This study investigated the role of Sphingomonas panaciterrae (PB20) on growth and nutritional profile of spinach applied through seed priming (SP), soil drenching (SD), foliar application (FA), and bacterial culture filtrate foliar (BCF) applications. The results showed that, depending on different methods of application, PB20 significantly increased plant height (19.57-65.65 %), fresh weight (7.26-37.41 %), total chlorophyll (71.14-192.54 %), carotenoid (67.10-211.67 %) antioxidant (55.99-207.04), vitamin C (8.1-94.6 %) and protein content (6.7-21.5 %) compared to control in the edible part of spinach. Among the mineral nutrients, root nitrogen (N) showed greater response to bacterial application (18.65%-46.15 % increase over control) than shoot nitrogen (6.70%-21.52 % increased over control). Likewise, in all methods of application, phosphorus (P) content showed significant increase over control both in root (42.79-78.48 %) and in shoot (3.57-27.0 %). Seed priming and foliar application of PB20 increased the shoot calcium (Ca) content compared to control. BCF foliar application yielded maximum magnesium (Mg), iron (Fe) and zinc (Zn) in shoot. However, seed priming resulted in maximum Fe in root. Overall, seed priming outperformed in growth, vitamin C, antioxidants, N and P uptake, while BCF foliar application resulted in better uptake of several nutrients. Multivariate analysis validated the positive association of most of the growth parameters with SP while several nutrients with FA and BCF. Based on the findings it is evident that this rhizobacteria PB20 has the potentiality to be applied as a biofertilizer to produce nutrient-enriched spinach with an improved yield. Farmers can conveniently incorporate PR20 through seed priming before planting of spinach, with additional benefits through foliar spray.

The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads

IMPORTANCE

Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.

Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA

1,1,1-Trichloro-2,2-bis(4-chlorophenyl)-ethane (DDT) is the first synthetic insecticide and one of the most widely used pesticides. The use of DDT has been banned, but it remains one of the most notorious environmental pollutants around the world. In this study, we found that γ-hexachlorocyclohexane (γ-HCH) dehydrochlorinase LinA from a γ-HCH-degrading bacterium, Sphingobium japonicum UT26, converts DDT to 1,1-dichloro-2,2-bis(4-chlorophenyl)-ethylene (DDE). Because of the weak DDT degradation activity of LinA, we could not detect such activity in UT26 cells expressing LinA constitutively. However, the linA-deletion mutant of UT26 harboring a plasmid for the expression of LinA, in which LinA was expressed at a higher level than UT26, showed the DDT degradation activity. This outcome highlights the potential for constructing DDT-degrading sphingomonad cells through elevated LinA expression.

Environmental exposure more than plastic composition shapes marine microplastic-associated bacterial communities in Pacific versus Caribbean field incubations

Microplastics have arisen as a global threat to marine ecosystems. In this study, we explored the role that plastic polymer type, incubation time and geographic location have on shaping the microbial community adhered to the microplastics, termed the plastisphere. We performed detailed bacterial plastisphere community analyses on microplastics of six different household plastic polymers, serving as proxies of secondary microplastics, incubated for 6 weeks in coastal Pacific waters. These bacterial communities were compared to the plastisphere communities grown on identical microplastic particles incubated in the coastal Caribbean Sea at Bocas del Toro, Panama. Ribosomal gene sequencing analyses revealed that bacterial community composition did not exhibit a significant preference for plastic type at either site but was instead driven by the incubation time and geographic location. We identified a 'core plastisphere' composed of 57 amplicon sequence variants common to all plastic types, incubation times and locations, with possible synergies between taxa. This study contributes to our understanding of the importance of geography in addition to exposure time, in the composition of the plastisphere.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus

Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.

Freshwater Cyanobacterial Toxins, Cyanopeptides and Neurodegenerative Diseases

Cyanobacteria produce a wide range of structurally diverse cyanotoxins and bioactive cyanopeptides in freshwater, marine, and terrestrial ecosystems. The health significance of these metabolites, which include genotoxic- and neurotoxic agents, is confirmed by continued associations between the occurrence of animal and human acute toxic events and, in the long term, by associations between cyanobacteria and neurodegenerative diseases. Major mechanisms related to the neurotoxicity of cyanobacteria compounds include (1) blocking of key proteins and channels; (2) inhibition of essential enzymes in mammalian cells such as protein phosphatases and phosphoprotein phosphatases as well as new molecular targets such as toll-like receptors 4 and 8. One of the widely discussed implicated mechanisms includes a misincorporation of cyanobacterial non-proteogenic amino acids. Recent research provides evidence that non-proteinogenic amino acid BMAA produced by cyanobacteria have multiple effects on translation process and bypasses the proof-reading ability of the aminoacyl-tRNA-synthetase. Aberrant proteins generated by non-canonical translation may be a factor in neuronal death and neurodegeneration. We hypothesize that the production of cyanopeptides and non-canonical amino acids is a more general mechanism, leading to mistranslation, affecting protein homeostasis, and targeting mitochondria in eukaryotic cells. It can be evolutionarily ancient and initially developed to control phytoplankton communities during algal blooms. Outcompeting gut symbiotic microorganisms may lead to dysbiosis, increased gut permeability, a shift in blood-brain-barrier functionality, and eventually, mitochondrial dysfunction in high-energy demanding neurons. A better understanding of the interaction between cyanopeptides metabolism and the nervous system will be crucial to target or to prevent neurodegenerative diseases.

Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii

Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.

Global transcriptional and translational regulation of Sphingomonas melonis TY in response to hyperosmotic stress

Hyperosmotic stress is one of the most ubiquitous stress factors in microbial habitats and impairs the efficiency of bacteria performing vital biochemical tasks. Sphingomonas serves as a 'superstar' of plant defense and pollutant degradation, and is widely existed in the environment. However, it is still unclear that how Sphingomonas sp. survives under hyperosmotic stress conditions. In this study, multiomics profiling analysis was conducted with S. melonis TY under hyperosmotic conditions to investigate the intracellular hyperosmotic responses. The transcriptome and proteome revealed that sensing systems, including most membrane protein coding genes were upregulated, genes related to two-component systems were tiered adjusted to reset the whole system, other stress response regulators such as sigma-70 were also significantly tiered upregulated. In addition, transport systems together with compatible solute biosynthesis related genes were significantly upregulated to accumulate intracellular nutrients and compatible solutes. When treated with hyperosmotic stress, redox-stress response systems were triggered and mechanosensitive channels together with ion transporters were induced to maintain cellular ion homeostasis. In addition, cellular concentration of c-di-guanosine monophosphate synthetase (c-di-GMP) was reduced, followed by negative influences on genes involved in flagellar assembly and chemotaxis pathways, leading to severe damage to the athletic ability of S. melonis TY, and causing detachments of biofilms. Briefly, this research revealed a comprehensive response mechanism of S. melonis TY exposure to hyperosmotic stress, and emphasized that flagellar assembly and biofilm formation were vulnerable to hyperosmotic conditions. Importance. Sphingomonas, a genus with versatile functions survives extensively, lauded for its prominent role in plant protection and environmental remediation. Current evidence shows that hyperosmotic stress as a ubiquitous environmental factor, usually threatens the survival of microbes and thus impairs the efficiency of their environmental functions. Thus, it is essential to explore the cellular responses to hyperosmotic stress. Hence, this research will greatly enhance our understanding of the global transcriptional and translational regulation of S. melonis TY in response to hyperosmotic stress, leading to broader perspectives on the impacts of stressful environments.

Dissecting giant hailstones: A glimpse into the troposphere with its diverse bacterial communities and fibrous microplastics

The formation of giant hailstones is a rare weather event that has devastating consequences in inhabited areas. This hazard has been occurring more frequently and with greater size of hailstones in recent years, and thus needs to be better understood. While the generally accepted mechanism is thought to be a process similar to the formation of smaller hailstones but with exceptional duration and stronger updrafts, recent evidence suggests that biotic and abiotic factors also influence the growth of these unusually large ice chunks. In this study, we improved these findings by determining the distribution of a wide variety of these factors throughout the hail volume and expanding the search to include new particles that are common in the environment and are of anthropogenic origin. We melted the concentric layers of several giant hailstones that fell to the ground over a small region in Slovenia in 2019. The samples, up to 13 cm in diameter, were analyzed for biotic and abiotic constituents that could have influenced their formation. Using 16S rRNA-based metagenomics approaches, we identified a highly diverse bacterial community, and by using scanning electron microscopy and Raman spectroscopy, we found natural and synthetic fibers concentrated in the cores of the giant hailstones. For the first time, we were able to detect the existence of microplastic fibers in giant hailstones and determine the changes in the distribution of sand within the volume of the samples. Our results suggest that changes in the composition of hail layers and their great diversity are important factors that should be considered in research. It also appears that anthropogenic microfiber pollutants were a significant factor in the formation of the giant hailstones analyzed in this study.

Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors

Large stocks of carbon and nitrogen stored in permafrost regions can potentially feed back to global biogeochemical cycles under climate warming. To understand the response of microbial communities to environmental changes, this study investigated the spatial distribution of bacterial communities in the upper layers (0-10, 10-20, and 20-30 cm) of seasonally frozen soil on the Tibetan Plateau and their relationships with the environmental factors. A total of 135 soil samples were collected from the soils at depths of 0-10, 10-20, and 20-30 cm in the Lhasa River and Nyang River basins, and the diversity and composition of bacterial communities in them were identified by high-throughput 16S rRNA gene sequencing. Bacterial diversity changed significantly with soil depth in the Nyang River basin (p < 0.001), while no obvious change was found in the Lhasa River basin. The whole bacterial composition exhibited small variations across different soil layers (p > 0.05). The relative abundance of aerobic bacteria, Sphingomonas and Arthrobacter, decreased with soil depth, while that of the other aerobic, facultative anaerobic, and anaerobic bacteria did not exhibit this trend. Soil pH was the key driving edaphic factor of the whole bacterial composition in all three depth layers, while vegetation also had an important influence on bacterial composition. Arthrobacter, Bradyrhizobium, and Bacillus had obvious correlations with soil nutrients or vegetation, while the other species were not significantly correlated with any environmental factors. Structural equation modeling revealed that vegetation and mean annual temperature had a key direct impact on the bacterial diversity and composition, respectively. Climate also indirectly affected bacterial communities, mainly through shaping soil pH and vegetation. These results indicate that the soil depth has a different impact on the bacterial α-diversity, whole bacterial composition, and specific taxa in the 0-30-cm surface layers of seasonally frozen soil, which were mainly determined by various environmental factors.

Bacterial oxidoreductive enzymes as molecular weapons for the degradation and metabolism of the toxic azo dyes in wastewater: a review

Azo dyes are extremely toxic and pose significant environmental and health risks. Consequently, mineralization and conversion to simple compounds are required to avoid their hazardous effects. A variety of enzymes from the bacterial system are thought to be involved in the degradation and metabolism of azo dyes. Bioremediation, a cost effective and eco-friendly biotechnology, involving bacteria is powered by bacterial enzymes. As mentioned, several enzymes from the bacterial system serve as molecular weapons in the degradation of these dyes. Among these enzymes, azoreductase, oxidoreductase, and laccase are of great interest for the degradation and decolorization of azo dyes. Combination of the oxidative and reductive enzymes is used for the removal of azo dyes from water. The aim of this review article is to provide information on the importance of bacterial enzymes. The review also discusses the genetically modified microorganisms in the biodegradation of azo dyes in polluted water.

Bacterial degradation of bisphenol analogues: an overview

Bisphenol A (BPA) is one of the most produced synthetic monomers in the world and is widespread in the environment. BPA was replaced by bisphenol analogues (BP) because of its adverse effects on life. Bacteria can degrade BPA and other bisphenol analogues (BP), diminishing their environmental concentrations. This study aimed to summarize the knowledge and contribute to future studies. In this review, we surveyed papers on bacterial degradation of twelve different bisphenol analogues published between 1987 and June 2022. A total of 102 original papers from PubMed and Google Scholar were selected for this review. Most of the studies (94.1%, n = 96) on bacterial degradation of bisphenol analogues focused on BPA, and then on bisphenol F (BPF), and bisphenol S (BPS). The number of studies on bacterial degradation of bisphenol analogues increased more than six times from 2000 (n = 2) to 2021 (n = 13). Indigenous microorganisms and the genera Sphingomonas, Sphingobium, and Cupriavidus could degrade several BP. However, few studies focussed on Cupriavidus. The acknowledgement of various aspects of BP bacterial biodegradation is vital for choosing the most suitable microorganisms for the bioremediation of a single BP or a mixture of BP.

Specific bacterial communities in the rhizosphere of low-cadmium and high‑zinc wheat (Triticum aestivum L.)

Microorganisms can modulate the contents of cadmium (Cd) and zinc (Zn) in wheat grains. Increasing the essential nutrient element Zn and decreasing the toxic element Cd in wheat grains can significantly improve human health. To characterize the specific bacterial communities associated with Cd and Zn accumulation in wheat, we conducted a field experiment by planting wheat cultivars differing in their capacity for Cd and Zn accumulation. The grain Cd contents in wheat cultivars YN23 (0.078 mg kg^-1), JN17 (0.080 mg kg^-1), YN836 (0.081 mg kg^-1) and LM2 (0.091 mg kg^-1) were significantly lower than those in ZM32 (0.16 mg kg^-1). The Zn contents were significantly higher in the grains of JN17 (44.36 mg kg^-1), LM2 (42.22 mg kg^-1) and ZM32 (43.19 mg kg^-1) than YN23 (27.05 mg kg^-1) and YN836 (29.70 mg kg^-1). On the basis of contents and bio-concentration factors of Cd and Zn in wheat grain, JN17 and LM2 were identified as low-Cd- and high-Zn-accumulating cultivars, YN23 and YN836 were low-Cd- and low-Zn-accumulating cultivars, and ZM23 was a high-Cd- and high-Zn-accumulating cultivar. The relative abundance values of Gemmatimonadaceae, Sphingomonadaceae and Beijerinckiaceae in the rhizospheres of low-Cd cultivars were significantly higher than those of high-Cd cultivars. High-Zn cultivars had higher abundance of Rhodanobacteraceae in the rhizosphere than did low-Zn cultivars. The low-Cd- and high-Zn-accumulating cultivars were enriched in Alphaproteobacteria and Gemmatimonadaceae, and strengthened nitrification function including aerobic_ammonia_oxidation and aerobic_nitrite_oxidation in the rhizosphere soil, thus contributing to the decreased Cd and increased Zn contents in wheat grains. Microbial technology is a promising method to control the contents of Cd and Zn in wheat grains.

Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health. The previously isolated phenanthrene-degrading bacterial consortium (PDMC) consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs. To identify the degradation mechanism of PAHs in the consortium PDMC, metagenomic binning was conducted and a Sphingomonadales assembly genome with 100% completeness was obtained. Additionally, Sphingobium sp. SHPJ-2, an efficient degrader of PAHs, was successfully isolated from the consortium PDMC. Strain SHPJ-2 has powerful degrading abilities and various degradation pathways of high-molecular-weight PAHs, including fluoranthene, pyrene, benzo[a]anthracene, and chrysene. Two ring-hydroxylating dioxygenases, five cytochrome P450s, and a pair of electron transfer chains associated with PAH degradation in strain SHPJ-2, which share 83.0%-99.0% similarity with their corresponding homologous proteins, were identified by a combination of Sphingomonadales assembly genome annotation, reverse-transcription quantitative polymerase chain reaction and heterologous expression. Furthermore, when coexpressed in Escherichia coli BL21(DE3) with the appropriate electron transfer chain, PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene, while PhnA2B2 degrade fluoranthene. Altogether, these results provide a comprehensive assessment of strain SHPJ-2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation.

Complete Genome Sequence of a Phage Infecting Sphingomonadaceae

We isolated a phage infecting a member of the Sphingomonadaceae family from a freshwater lake. The phage has a DNA genome of 41,771 bp, with a GC content of 61.7%. The genome harbors 50 predicted protein-coding genes and an auxiliary metabolic gene, which encodes a protein belonging to the radical S-adenosylmethionine superfamily.

Draft Genome Sequences of Sphingomonadaceae Strains Isolated from a Freshwater Lake

We isolated two bacterial strains (Sphingomonadaceae family) from Lake Biwa, Japan. Based on whole-genome sequencing results, one strain (BSN-002) was assigned to the Sphingopyxis genus and the other (BSN-004) to Sphingomonas aquatilis.

Phenanthrene-degrading Sphingobium xenophagum are widely distributed in the western Pacific Ocean

Six phenanthrene-degrading bacteria were isolated from surface sea water sampled from the western Pacific Ocean. They were identified as Sphingobium xenophagum (formerly Sphingomonas xenophaga) based on morphological, biochemical, and chemical characteristics and 16S rRNA sequences. Salinity ranges for the growth of these isolates were broader than those of seven reported Sphingomonas strains isolated from soil, and the optimum NaCl concentration in the growth medium was higher than that for soil sphingomonads. These isolates also exhibited higher phenanthrene-degrading activity in briny conditions than that of a phenanthrene-degrading Sphingomonas strain isolated from soil. A DNA fragment carrying nah genes, which are encoded on the naphthalene-catabolic plasmid NAH of Pseudomonas putida PpG7, hybridised less strongly with the total DNA of all isolates. Certain genes for phenanthrene degradation were also preliminarily characterised in all isolates. This is the first demonstration that S. xenophagum strains, that are able to degrade phenanthrene, are widely distributed in marine environments, and the growth and phenanthrene-degrading activity of these strains are adapted to briny conditions. Results also suggest that genes for phenanthrene degradation, which are dissimilar to the nah genes, were also ubiquitously distributed in marine strains.

Bisphenol A biodegradation by Sphingonomas sp. YK5 is regulated by acyl-homoserine lactone signaling molecules

Microbial degradation is an effective approach for the removal of Bisphenol A (BPA). During the biodegradation process, quorum sensing (QS) is a phenomenon that enables bacteria to coordinate collective behaviors based on cell density-dependent chemical signals. However, whether the degradation of BPA can be facilitated by this QS system (such as acyl-homoserine lactone, AHL) is unclear. To answer this question, the bifunctional Sphingonomas sp. strain YK5 that had BPA-degrading and AHL-producing properties was used. Biochemical analysis revealed that this bacterial strain mainly produced C8-HSL signals. Gene knockout experiments indicated that the AHL-system (LuxI1/LuxI2) was required for efficient BPA degradation. RT-PCR analyses revealed that the AHL system positively regulated the relative expression of genes (bisdA, CYP450, hapA, ligAB, and proB) involved in BPA degradation. Given that AHL signaling may be a common trait among BPA-degrading microorganisms and AHL system can regulate the degradation activity, manipulation of this system may be a valuable strategy to control BPA biodegradation.

Sphingomonas and Phenylobacterium as Major Microbiota in Thymic Epithelial Tumors

The microbiota has been reported to be closely associated with carcinogenesis and cancer progression. However, its involvement in the pathology of thymoma remains unknown. In this study, we aimed to identify thymoma-specific microbiota using resected thymoma samples. Nineteen thymoma tissue samples were analyzed through polymerase chain reaction amplification and 16S rRNA gene sequencing. The subjects were grouped according to histology, driver mutation status in the GTF2I gene, PD-L1 status, and smoking habits. To identify the taxa composition of each sample, the operational taxonomic units (OTUs) were classified on the effective tags with 97% identity. The Shannon Index of the 97% identity OTUs was calculated to evaluate the alpha diversity. The linear discriminant analysis effect size (LEfSe) method was used to compare the relative abundances of all the bacterial taxa. We identified 107 OTUs in the tumor tissues, which were classified into 26 genera. Sphingomonas and Phenylobacterium were identified as abundant genera in almost all the samples. No significant difference was determined in the alpha diversity within these groups; however, type A thymoma tended to exhibit a higher bacterial diversity than type B thymoma. Through the LEfSe analysis, we identified the following differentially abundant taxa: Bacilli, Firmicutes, and Lactobacillales in type A thymoma; Proteobacteria in type B thymoma; Gammaproteobacteria in tumors harboring the GTF2I mutation; and Alphaproteobacteria in tumors without the GTF2I mutation. In conclusion, Sphingomonas and Phenylobacterium were identified as dominant genera in thymic epithelial tumors. These genera appear to comprise the thymoma-specific microbiota.

Investigations on the Degradation of the Bile Salt Cholate via the 9,10-Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11

Bile salts such as cholate are steroid compounds from the digestive tracts of vertebrates, which enter the environment upon excretion, e.g., in manure. Environmental bacteria degrade bile salts aerobically via two pathway variants involving intermediates with Δ^1,4- or Δ^4,6-3-keto-structures of the steroid skeleton. Recent studies indicated that degradation of bile salts via Δ^4,6-3-keto intermediates in Sphingobium sp. strain Chol11 proceeds via 9,10-seco cleavage of the steroid skeleton. For further elucidation, the presumptive product of this cleavage, 3,12β-dihydroxy-9,10-seco-androsta-1,3,5(10),6-tetraene-9,17-dione (DHSATD), was provided to strain Chol11 in a co-culture approach with Pseudomonas stutzeri Chol1 and as purified substrate. Strain Chol11 converted DHSATD to the so far unknown compound 4-methyl-3-deoxy-1,9,12-trihydroxyestra-1,3,5(10)7-tetraene-6,17-dione (MDTETD), presumably in a side reaction involving an unusual ring closure. MDTETD was neither degraded by strains Chol1 and Chol11 nor in enrichment cultures. Functional transcriptome profiling of zebrafish embryos after exposure to MDTETD identified a significant overrepresentation of genes linked to hormone responses. In both pathway variants, steroid degradation intermediates transiently accumulate in supernatants of laboratory cultures. Soil slurry experiments indicated that bacteria using both pathway variants were active and also released their respective intermediates into the environment. This instance could enable the formation of recalcitrant steroid metabolites by interspecies cross-feeding in agricultural soils.

Complete Genome Sequence of Sphingobium xenophagum PH3-15, Isolated from La Roche-Posay Thermal Water Sources

We report here the complete genome sequence of Sphingobium xenophagum strain PH3-15, which was isolated from La Roche-Posay thermal water sources. The assembled 4.6-Mbp genome consisted of two chromosomes and three plasmids. These data will provide valuable information and important insights into the physiology and metabolism of this Sphingobium organism.

Comparative microbial antibiotic resistome between urban and deep forest environments

A paradoxical result of using antibiotics to eradicate microbial pathogens is the emergence of a vast number of resistant microbes in various environments. The concern that environmental microbes will inevitably become resistant to virtually every clinically usable antibiotics has been exacerbated by the spread of these resistance genes across different environments and the emergence of multidrug resistant phenotypes. Here, we provide metagenomic insights into the microbiomes and resistomes of 16 soil samples collected from hospitals, residential areas, and forest parks in the megacity of Beijing and deep forests in the Yunnan province. Using Illumina HiSeq sequencing, we investigated the microbial diversity within the metagenomic shotgun reads and identified 486 antibiotic-resistant genes (ARGs) classified into 30 types from these samples, among which multidrug resistance genes were the most abundant. Our results present an important reference and direct comparison of microbial antibiotic resistomes of soil samples from a megacity and deep forests and extend our understanding of the spread of ARGs in modern urban and natural environments.

Transcriptome analysis expands the potential roles of quorum sensing in biodegradation and physiological responses to microcystin

Bacterial degradation is one of the most efficient ways to remove microcystins (MCs), the most frequently detected toxin in cyanobacterial blooms. Using Novosphingobium sp. ERW19 as a representative strain, our laboratory previously demonstrated that quorum sensing (QS), the cell density-dependent gene regulation system, positively regulates biodegradation of MCs via transcriptional activation of mlr-pathway-associated genes. Increasing evidence indicates that QS is involved in a wide spectrum of regulatory circuits, but it remains unclear which physiological processes in MC degradation besides the expression of MC-degrading genes are also subject to QS-dependent regulation. This study used transcriptome analysis to identify QS-regulated genes during degradation of MCs. A large percentage (up to 32.6%) of the genome of the MC-degrading bacterial strain Novosphingobium sp. ERW19 was significantly differentially expressed in the corresponding QS mutants. Pathway enrichment analysis of QS-regulated genes revealed that QS mainly influenced metabolism-associated pathways, particularly those related to amino acid metabolism, carbohydrate metabolism, and biodegradation and metabolism of xenobiotics. In-depth functional interpretation of QS-regulated genes indicated a variety of pathways were potentially associated with bacterial degradation or physiological responses to MCs, including genes involved in cell motility, cytochrome P450-dependent metabolism of xenobiotics, glutathione S-transferase (GST), envelope stress response, and ribosomes. Furthermore, QS may be involved in regulating the initial and final steps of the catabolic pathway of phenylacetic acid, an intermediate product of MC degradation. Collectively, this global survey of QS-regulated genes in a MC-degrading bacterial strain facilitates a deeper understanding of QS-controlled processes that may be important for bacterial degradation of MCs or may contribute to the physiological responses of bacteria to MCs.

Triazophos and its metabolite diethyl phosphate have different effects on endocrine hormones and gut health in rats

Organophosphorus pesticide (OP) residues present in food can be metabolized into diethylphosphate (DEP) in vivo. Epidemiological studies of OPs have usually focused on these metabolites, while animal studies mainly assessed the OPs. Here, we compared the health risks of a frequently detected OP, triazophos (TAP), and its major metabolite, DEP, in rats. Levels of serum lipids and, sex hormones were measured using immunoassay kits. Gut hormones and inflammatory cytokines were assessed using a multiplexing kit, and the gut microbiota was evaluated by 16S rRNA gene sequencing. After a 24-week exposure period, both TAP and DEP significantly decreased serum levels of triglycerides, cholesterol, low-density lipoprotein cholesterol, and IL-6 (p < 0.05). However, DEP exposure had a stronger effect on serum estradiol (p < 0.05) than TAP, whereas only TAP inhibited the secretion of gut hormones. Both TAP and DEP enriched the pathogenic genera Oscillibacter, Peptococcus and Paraprevotella in the gut, and TAP also enriched enteritis-related genera Roseburia and Oscillibacter, which may affect the secretion of gut hormones. These findings indicate that the use of dialkyl phosphates as markers of OPs to examine the correlations of OP exposure with diseases may only provide partial information, especially for diseases related to gut health and the endocrine system.

Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability

The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.

Biotreatment and bacterial succession in an upflow immobilized cell bioreactor fed with fludioxonil wastewater

The large quantities and the persistent nature of fungicide wastewaters have increased the efforts towards a sustainable technological solution. In this context, fludioxonil-contaminated wastewater was treated in an upflow immobilized cell bioreactor, resulting in chemical oxygen demand (COD) removal efficiency even higher than 80%, whereas the electrical conductivity (EC) of the effluent was gradually increased. Organic-F was mineralized by 94.0 ± 5.2%, which was in accordance with the high fludioxonil removal efficiency (95.4 ± 4.0%). In addition, effluent total Kjeldahl nitrogen (TKN) concentration reduced significantly during bioprocessing. A strong relationship among COD removal, TKN/total nitrogen removal, and effluent EC increase (p < 0.01) was identified. Despite the adequate aeration provided, effluent nitrite and nitrate concentrations were negligible. Illumina sequencing revealed a reduction in the relative abundances of Betaproteobacteria, Chloroflexi, Planctomycetes, and Firmicutes and an increase in the proportion of Alphaproteobacteria and Actinobacteria. A shift in bacterial communities occurred during fludioxonil treatment, resulting in the significant increase of the relative abundances of Empedobacter, Sphingopyxis, and Rhodopseudomonas (from 0.67 ± 0.13% at the start-up to 34.34 ± 1.60% at the end of biotreatment). In conclusion, the immobilized cell bioreactor permitted the proliferation of specialized activated sludge microbiota with an active role in the depuration of postharvest fungicides.

Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive subculturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, Sphingobium and Pseudomonas, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Coexisting genera Achromobacter and Cupriavidus maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism, which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering Sphingobium and Pseudomonas spp. utilized relatively water-insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in the creation of niches in response to diesel fuel exposure which were created through the production of more-water-soluble biotransformation products available to cocolonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.IMPORTANCE There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification, which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for the biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed, which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.

Comparative genomic analysis of iprodione-degrading Paenarthrobacter strains reveals the iprodione catabolic molecular mechanism in Paenarthrobacter sp. strain YJN-5

Degradation of the fungicide iprodione by the Paenarthrobacter sp. strain YJN-5 is initiated via hydrolysis of its N1 amide bond to form N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine. In this study, another iprodione-degrading strain, Paenarthrobacter sp. YJN-D, which harbours the same metabolic pathway as strain YJN-5 was isolated and characterized. The genes that encode the conserved iprodione catabolic pathway were identified based on comparative analysis of the genomes of the two iprodione-degrading Paenarthrobacter sp. and subsequent experimental validation. These genes include an amidase gene, ipaH (previously reported in AEM e01150-18); a deacetylase gene, ddaH, which is responsible for hydantoin ring cleavage of N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine, and a hydrolase gene, duaH, which is responsible for cleavage of the urea side chain of (3,5-dichlorophenylurea)acetic acid, thus yielding 3,5-dichloroaniline as the end product. These iprodione-catabolic genes are distributed on three plasmids in strain YJN-5 and are highly conserved between the two iprodione-degrading Paenarthrobacter strains. However, only the ipaH gene is flanked by a mobile genetic element. Two iprodione degradation cassettes bearing ipaH-ddaH-duaH were constructed and expressed in strains Pseudomonas putida KT2440 and Bacillus subtilis SCK6 respectively. Our findings enhance the current understanding of the microbial degradation mechanism of iprodione.

Sphingosinithalassobacter tenebrarum sp. nov., isolated from a deep-sea cold seep

A Gram-stain-negative, facultatively anaerobic, yellow-pigmented, non-motile, rod-shaped bacterium, designated zrk23^T, was isolated from a deep-sea cold seep. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences placed zrk23^T within the genus Sphingosinithalassobacter and showed the highest similarity to Sphingosinithalassobacter portus FM6^T (97.93 %). Growth occurs at temperatures from 16 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.5 (optimum, pH 7.0) and in 0-5.0 % (w/v) NaCl (optimum, 1.5 %). The major fatty acids were C_16 : 0, C_14 : 0 2-OH and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phosphoglycolipid, three unidentified glycolipids and three unidentified phospholipids. The G+C content of the genomic DNA was 64.69 %. The average nucleotide identity values between zrk23^T and the most closely related available genome, of Sphingosinithalassobacter portus FM6^T, was 82.21 %, indicating that zrk23^T was clearly distinguished from S. portus. The analysis of genome sequence of zrk23^T revealed that there were many genes associated with degradation of aromatic compounds existing in the genome of zrk23^T. As a result of the combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, zrk23^T was considered to represent a novel species of the genus Sphingosinithalassobacter, for which the name Sphingosinithalassobacter tenebrarum sp. nov. is proposed. The type strain is zrk23^T (=KCTC 72896^T=MCCC 1K04416^T).

Genetic and physiological analysis of biofilm formation on different plastic surfaces by Sphingomonas sp. strain S2M10 reveals an essential function of sphingan biosynthesis

Alphaproteobacteria belonging to the group of the sphingomonads are frequently found in biofilms colonizing pure-water systems, where they cause technical and hygienic problems. In this study, physiological properties of sphingomonads for biofilm formation on plastic surfaces were analysed. Sphingomonas sp. strain S2M10 was isolated from a used water-filtration membrane and submitted to transposon mutagenesis for isolating mutants with altered biofilm formation. Mutants showing strongly decreased biofilm formation carried transposon insertions in genes for the biosynthesis of the polysaccharide sphingan and for flagellar motility. Flagella-mediated attachment was apparently important for biofilm formation on plastic materials of intermediate hydrophobicity, while a mutant with defect in spnB, encoding the first enzyme in sphingan biosynthesis, showed no biofilm formation on all tested materials. Sphingan-dependent biofilm formation was induced in the presence of specific carbon sources while it was not induced in complex medium with yeast extract and tryptone. The regulation of sphingan-based biofilm formation was investigated by interfering with the CckA/ChpT/CtrA phosphorelay, a central signal-transduction pathway in most Alphaproteobacteria. Construction and ectopic expression of a kinase-deficient histidine kinase CckA caused cell elongation and massive sphingan-dependent cell aggregation. In addition, it caused increased activity of the promotor of spnB. In conclusion, these results indicate that sphingan-based biofilm formation by sphingomonads might be triggered by specific carbon sources under prototrophic conditions resembling a milieu that often prevails in pure-water systems.

The LuxI/LuxR-Type Quorum Sensing System Regulates Degradation of Polycyclic Aromatic Hydrocarbons via Two Mechanisms

Members of the Sphingomonadales are renowned for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). However, little is known about the regulatory mechanisms of the degradative pathway. Using cross-feeding bioassay, a functional LuxI/LuxR-type acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) system was identified from Croceicoccus naphthovorans PQ-2, a member of the order Sphingomonadales. Inactivation of the QS system resulted in a significant decrease in PAHs degradation. The QS system positively controlled the expression of three PAH-degrading genes (ahdA1e, xylE and xylG) and a regulatory gene ardR, which are located on the large plasmid. Interestingly, the transcription levels of these three PAH-degrading genes were significantly down-regulated in the ardR mutant. In addition, bacterial cell surface hydrophobicity and cell morphology were altered in the QS-deficient mutant. Therefore, the QS system in strain PQ-2 positively regulates PAH degradation via two mechanisms: (i) by induction of PAH-degrading genes directly and/or indirectly; and (ii) by an increase of bacterial cell surface hydrophobicity. The findings of this study improve our understanding of how the QS system influences the degradation of PAHs, therefore facilitating the development of new strategies for the bioremediation of PAHs.

Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

Dynamics and response of microbial diversity to nutritional conditions in denitrifying bioreactor for linear alkylbenzene sulfonate removal

The aim of this study was to evaluate the microbial structure and phylogenetic diversity under the influence of nutritional conditions and hydraulic retention time (HRT) in fluidized bed reactors (FBR), operated in short HRT (8 h - FBR8; 12 h - FBR12) for linear alkylbenzene sulfonate (LAS) removal from laundry wastewater. After each phase, biofilm samples from FBR8 and FBR12 were submitted to microbial sequencing by Mi-Seq Illumina®. Higher LAS removal rates were observed after 313 days, achieving 99 ± 3% in FBR12 (22.5 ± 5.9 mg LAS/L affluent) and 93 ± 12% in FBR8 (20.6 ± 4.4 mg LAS/L affluent). Different modifications involving genera of bacteria were observed throughout the reactors operation. The identified microorganisms were, mostly, related to LAS degradation and nitrogen conversion such as Dechloromonas, Flavobacterium, Pseudomonas, and Zoogloea.

Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae, we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus, is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae, for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae.

Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions

Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO₂-dependent and accompanied with CO₂ incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO₂-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.