Benzene degradation by Ralstonia pickettii PKO1 in the presence of the alternative substrate succinate

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.

Sulfamethoxazole is Metabolized and Mineralized at Extremely Low Concentrations

The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the range of μg L-1. Many are biotransformed by cometabolic mechanisms; however, there is scarce information concerning their direct metabolization in this concentration range. Threshold concentrations for microbial assimilation have been reported in both pure and mixed cultures from different origins. The literature suggests a range value for bacterial growth of 1-100 μg L-1 for isolated aerobic heterotrophs in the presence of a single substrate. We aimed to investigate, as a model case, the threshold level for sulfamethoxazole (SMX) metabolization in pure cultures of Microbacterium strain BR1. Previous research with this strain has covered the milligram L-1 range. In this study, acclimated cultures were exposed to concentrations from 0.1 to 25 μg L-1 of 14C-labeled SMX, and the 14C-CO2 produced was trapped and quantified over 24 h. Interestingly, SMX removal was rapid, with 98% removed within 2 h. In contrast, mineralization was slower, with a consistent percentage of 60.0 ± 0.7% found at all concentrations. Mineralization rates increased with rising concentrations. Therefore, this study shows that bacteria are capable of the direct metabolization of organic micropollutants at extremely low concentrations (sub μg L-1).

Biodegradation of microplastics derived from controlled release fertilizer coating: Selective microbial colonization and metabolism in plastisphere

Coated controlled-release fertilizers (CRFs) are widely used in agriculture, and the persistent presence of residual polymer coating has raised environmental concerns. This study investigates the underlying degradation dynamics of microplastics (MPs) derived from three typical materials used in CRFs, including polyethylene (PE), epoxy (EP), and polyurethane (PU), through a soil degradation test. The formation of surface biofilm, the succession process, and metabolic characteristics of microbial community are revealed by laser scanning confocal microscope, 16S rRNA sequencing, and non-targeted metabolomics analysis. The weight loss rates of PE, EP, and PU after 807 days of degradation were 16.70 %, 2.79 %, and 4.86 %, respectively. Significant secondary MPs were produced with tears and holes appeared in the coating cross sections and pyrolysis products were produced such as ethers, acids, and esters for PE; alkanes, olefins and their branched-chain derivatives for EP; and short-chain fatty acids and benzene molecules for PU. The coating surface selectively recruited the bacteria of Chujaibacter and Ralstonia and fungus of Fusarium and Penicillium, forming biofilm composed of lipids, proteins, and living cells. The metabolism of amino acids and polymers was enhanced to protect against MP-induced stress. The metabolites or intermediates of organic acids and derivatives, oxygen-contained organic compounds, and benzenoids on CRF surface increased significantly compared with soil, but there were no significant differences among different coating types. This study provides insights to the underlying mechanisms of biodegradation and microenvironmental changes of MPs in soil.

Tea biochar-immobilized Ralstonia Bcul-1 increases nitrate nitrogen content and reduces the bioavailability of cadmium and chromium in a fertilized vegetable soil

Pyrolytic biochar (PL-BC, pyrochar) and hydrothermal biochar (HT-BC, hydrochar) derived from branches and leaves of tea plants had different pH, electrical conductivity (EC), total carbon nitrogen content, BET surface area, total pore volume, average pore diameter, and functional groups. HT-BC had a larger specific surface area and more functional groups than PL-BC. Ralstonia Bcul-1 (R-B) was the dominant and functional bacteria in a fertilized vegetable soil supplemented with TBB-immobilized R-B (TBB + R-B). R-B vitality was more closely related to BET surface area, total pore volume, and functional groups of tea-based biochar (TBB: PL-BC and HT-BC). R-B was able to maintain high oxidase activity. R-B and TBB + R-B can increase the activities of urease and peroxidase in vegetable soil playing an essential role in the biotransformation of ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N). TBB was able to simultaneously increase the content of NO₃^--N and NH₄⁺-N, and TBB + R-B also significantly increased NO₃^--N content but decreased NH₄⁺-N content in a fertilized vegetable soil. These results indicated that R-B promoted nitrification in the soil, i.e. conversion of NH₄⁺-N into NO₃^--N, by enhancing the activities of urease and peroxidase. R-B had high adsorption capacity for cadmium (Cd) and chromium (Cr) (Cd&Cr: Cd and Cr). Moreover, TBB + R-B was able to convert weak acid extractable and reducible Cd&Cr into a more stable residual fraction and oxidizable Cd&Cr. The overall effect of the treatments was to reduce plant uptake of Cd&Cr by cabbage. TBB + R-B significantly promoted R-B growth, changed inorganic nitrogen speciation, increased NO₃^--N supply, reduced Cd&Cr bioavailability, and decreased plant tissue Cd&Cr content.

Identification of a novel heavy metal resistant Ralstonia strain and its growth response to cadmium exposure

A novel Ralstonia Bcul-1 strain was isolated from soil samples that was closest to Ralstonia pickettii. Broad-spectrum resistance was identified to a group of heavy metal ions and tolerance to concentrations of Cd²⁺ up to 400 mg L^-1. Low concentrations of heavy metal ions did not have distinctive impact on heavy metal resistance genes and appeared to induce greater expression. Under exposure to Cd²⁺, cell wall components were significantly enhanced, and some proteins were also simultaneously expressed allowing the bacteria to adapt to the high Cd²⁺ living environment. The maximum removal rate of Cd²⁺ by the Ralstonia Bcul-1 strain was 78.97% in the culture medium supplemented with 100 mg L^-1 Cd²⁺. Ralstonia Bcul-1 was able to survive and grow in a low nutrient and cadmium contaminated (0.42 mg kg^-1) vegetable soil, and the cadmium removal rate was up to 65.76% in 9th growth. Ralstonia Bcul-1 mixed with biochar could maintain sustainable growth of this strain in the soil up to 75 d and the adsorption efficiency of cadmium increased by 16.23-40.80% as compared to biochar application alone. Results from this work suggests that Ralstonia Bcul-1 is an ideal candidate for bioremediation of nutrient deficient heavy metal contaminated soil.

BTEX biodegradation by Bacillus amyloliquefaciens subsp. plantarum W1 and its proposed BTEX biodegradation pathways

Benzene, toluene, ethylbenzene and (p-, m- and o-) xylene (BTEX) are classified as main pollutants by several environmental protection agencies. In this study, a non-pathogenic, Gram-positive rod-shape bacterium with an ability to degrade all six BTEX compounds, employed as an individual substrate or as a mixture, was isolated. The bacterial isolate was identified as Bacillus amyloliquefaciens subsp. plantarum strain W1. An overall BTEX biodegradation (as individual substrates) by strain W1 could be ranked as: toluene > benzene, ethylbenzene, p-xylene > m-xylene > o-xylene. When presented in a BTEX mixture, m-xylene and o-xylene biodegradation was slightly improved suggesting an induction effect by other BTEX components. BTEX biodegradation pathways of strain W1 were proposed based on analyses of its metabolic intermediates identified by LC–MS/MS. Detected activity of several putative monooxygenases and dioxygenases suggested the versatility of strain W1. Thus far, this is the first report of biodegradation pathways for all of the six BTEX compounds by a unique bacterium of the genus Bacillus. Moreover, B. amyloliquefaciens subsp. plantarum W1 could be a good candidate for an in situ bioremediation considering its Generally Recognized as Safe (GRAS) status and a possibility to serve as a plant growth-promoting rhizobacterium (PGPR).

Exploring Antifouling Activity of Biosurfactants Producing Marine Bacteria Isolated from Gulf of California

Biofouling causes major problems and economic losses to marine and shipping industries. In the search for new antifouling agents, marine bacteria with biosurfactants production capability can be an excellent option, due to the amphipathic surface-active characteristic that confers antimicrobial and antibiofilm activities. The aim of this study was to evaluate the antifouling activity of biosurfactants producing marine bacteria from the Gulf of California. The cell free culture supernatant (CFCS) of Bacillus niabensis (S-69), Ralstonia sp. (S-74) (isolated from marine sediment) and of B. niabensis (My-30) (bacteria associated to the sponge Mycale ramulosa) were screened for production of biosurfactants (using hemolysis and drop collapse test, oil displacement and emulsifying activity). The toxicity and antifouling activity were evaluated against biofoulers (bacteria forming biofilm and macrofoulers) both in laboratory and field assays. The results indicate that all bacteria were biosurfactant producers, but the higher capability was shown by B. niabensis (My-30) with high emulsifying properties (E24) of 71%. The CFCS showed moderate toxicity but were considered non-toxic against Artemia franciscana at low concentrations. In the antifouling assay, the CFCS of both strains of B. niabensis showed the best results for the reduction of the biofilm formation (up 50%) against all Gram-positive bacteria and most Gram-negative bacteria with low concentrations. In the field assay, the CFCS of B. niabensis (My-30) led to the reduction of 30% of biofouling compared to the control. The results indicate that the biosurfactant produced by B. niabensis (My-30) has promising antifouling activity.

Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants

On-line detection of aromatic hydrocarbon pollutants in aqueous environments can be achieved by biosensing strains having fusion of gene responsible for pollutant sensing protein with a reporter gene. Regulatory proteins TbuT, HbpR and PhnR are such proteins for recognizing one-, two-and three-ring aromatic hydrocarbon pollutants respectively, for which the structure is not known till date. Aim of the present study was to predict the structure of proteins and to determine their in-silico interaction with array of pollutants. Structure prediction of proteins was performed using I-TASSER and Phyre2 and refined with ModRefiner and 3DRefine. Total 14 models were obtained for each protein and the best model had more than 95% coverage in Ramachandran plot region. After successful structure prediction, molecular interaction of proteins with respective aromatic hydrocarbon pollutants categorized by United States Environmental Protection Agency was studied using AutoDockVina where the binding energy was found to fall in range of -4.6 to -8.4 kcal/mol. The types of protein-pollutant interaction were analyzed by LigPlus and Discovery Studio 2017 R2 Client which were found to be similar for standard and pollutant compounds. This study enables us to predict the range of pollutants possible to be detected using these regulatory protein-based biosensors.

Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1

Exploring adaptive strategies by which microorganisms function and survive in low-energy natural environments remains a grand goal of microbiology, and may help address a prime challenge of the 21st century: degradation of man-made chemicals at low concentrations (“micropollutants”). Here we explore physiological adaptation and maintenance energy requirements of a herbicide (atrazine)-degrading microorganism (Arthrobacter aurescens TC1) while concomitantly observing mass transfer limitations directly by compound-specific isotope fractionation analysis. Chemostat-based growth triggered the onset of mass transfer limitation at residual concentrations of 30 μg L⁻¹ of atrazine with a bacterial population doubling time (t_d) of 14 days, whereas exacerbated energy limitation was induced by retentostat-based near-zero growth (t_d = 265 days) at 12 ± 3 μg L⁻¹ residual concentration. Retentostat cultivation resulted in (i) complete mass transfer limitation evidenced by the disappearance of isotope fractionation (ε¹³C = −0.45‰ ± 0.36‰) and (ii) a twofold decrease in maintenance energy requirement compared with chemostat cultivation. Proteomics revealed that retentostat and chemostat cultivation under mass transfer limitation share low protein turnover and expression of stress-related proteins. Mass transfer limitation effectuated slow-down of metabolism in retentostats and a transition from growth phase to maintenance phase indicating a limit of ≈10 μg L⁻¹ for long-term atrazine degradation. Further studies on other ecosystem-relevant microorganisms will substantiate the general applicability of our finding that mass transfer limitation serves as a trigger for physiological adaptation, which subsequently defines a lower limit of biodegradation.

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing

To improve the understanding of bacterial community in heavy metals contaminated soils, we studied the effects of environmental factors on the bacterial community structure in contaminated fields located in Shaanxi Province of China. Our results showed that microbial community structure varied among sites, and it was significantly affected by soil environmental factors such as pH, soil organic matter (SOM), Cd, Pb and Zn. In addition, Spearman's rank-order correlation indicated heavy metal sensitive (Ralstonia, Gemmatimona, Rhodanobacter and Mizugakiibacter) and tolerant (unidentified-Nitrospiraceae, Blastocatella and unidentified-Acidobacteria) microbial groups. Our findings are crucial to understanding microbial diversity in heavy metal polluted soils of China and can be used to evaluate microbial communities for scientific applications such as bioremediation projects.

Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions

Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.

Diazinon degradation by a novel strain Ralstonia sp. DI-3 and X-ray crystal structure determination of the metabolite of diazinon

Diazinon is a widely used organophosphorus insecticide often detected in the environment. A highly effective diazinon-degrading Ralstonia sp. strain DI-3 was isolated from agricultural soil. Strain DI-3 can utilize dimethoate as its sole carbon source for growth and degrade an initial concentration of 100 mg L-1 diazinon to non-detectable levels within 60 h in liquid culture. A small amount of second carbon source as co-substrate could slightly enhance the biodegradation of diazinon. In addition, a less toxic metabolic intermediate formed during the degradation of diazinon mediated by strain DI-3 was purified using thin-layer chromatography (TLC) and identified based on single-crystal Xray diffraction analysis, allowing a degradation pathway for diazinon by pure culture to be proposed. Finally, this is the first providing authentic evidence to describe the metabolite.

Isolation, identification and characterization of a novel Ralstonia sp. FD-1, capable of degrading 4-fluoroaniline

A gram-negative strain, designated as FD-1, isolated from aerobic activated sludge was capable of metabolizing 4-fluoroaniline (4-FA) as its sole carbon and nitrogen source and energy supply. According to the Biolog GNIII detection method 17 of 71 carbon substrates were easily utilized, while 12 of 23 substrates did not inhibit strain FD-1. The 16S rDNA sequence from strain FD-1 was 99 % similar to Ralstonia sp., suggesting that it belonged to the genus Ralstonia. The optimal conditions for growth and 4-FA degradation were pH 7 and 30 °C. The tolerance to 4-FA were 1,250 mg/L, while the tolerance to salinity was 15 g/L. Catechol 2,3-dioxygenase activity was detected and degradation intermediates were analyzed by liquid chromatography mass spectrometry leading to a proposed degradation pathway and suggesting that extradiol cleavage was involved in 4-FA degradation. This is the first report on the degradation of 4-FA by a bacterium from the Ralstonia genus.

Utilization of pyrene and benzoate in Mycobacterium isolate KMS is regulated differentially by catabolic repression

The soil isolate, Mycobacterium sp. strain KMS, utilizes an array of carbon compounds including the aromatics benzoate and pyrene as sole carbon sources. Growth on pyrene induced both chromosomal and plasmid nidA genes encoding pyrene ring-hydroxylating dioxygenase α-subunits for pyrene oxidation. Diauxic growth occurred when KMS was cultured with pyrene plus either acetate, succinate, fructose, or benzoate and nidA expression only was detected in the second slower log-phase period. Potential cAMP-CRP binding sites exist within the promoter region of both nidA genes indicating that cAMP-CRP may be involved in catabolite repression of pyrene utilization. When cultured with benzoate plus either acetate, succinate, or fructose, there was no diauxic growth. Also there was no diauxic growth on fructose plus succinate or acetate. Expression of a benA gene, encoding a benzoate dioxygenase α-subunit involved in the initiation of benzoate oxidation, was detected in log-phase cells from the benzoate-mixed substrate cultures at the same level as when the cells were cultured on benzoate alone. These findings suggested that catabolite repression of pyrene but not benzoate occurred in isolate KMS. These differences may help the microbe exploit the varied carbon sources available in the soil and rhizosphere environments.

How to live at very low substrate concentration

Availability of carbon/energy sources and temperature are the two environmental factors that severely restrict heterotrophic growth in most ecosystems. DOC concentrations in ground, drinking and surface waters are typically in the range of 0.5-5 mg/L, but most of this is present in a polymeric, inaccessible form for microbes. Concentrations of microbiologically available carbon compounds (so-called assimilable organic carbon, AOC) are usually in the range of 10-100 μg/L, those of individual sugars or amino acids are not higher than a few μg/L. Until recently microbiologists assumed that such nutrient-poor (oligotrophic) environments are "deserts" for life, and that the majority of bacterial cells seen in the microscope are dead, dormant or at least severely starved. Nevertheless, despite the low concentrations of available carbon compounds, bacterial cell numbers recorded in these environments typically are in the range of 10(5)-10(6) per mL. Over the last years, we have learnt that most of these microbes are perfectly alive, metabolizing and ready to grow when given the chance. Hence, microbes have adapted and developed strategies to cope with this situation. Laboratory studies with pure cultures suggest that bacterial cells have developed two strategies to live under such conditions. The first strategy is to perform a "multivorous" way of life by taking up and metabolizing dozens of different carbon substrates simultaneously (i.e., they are NOT specializing on a particular substrate, which they can take up with very high affinity). This "mixed substrate growth" equips the cell with a kinetic advantage and metabolic flexibility. Simultaneous utilization of a multitude of carbon substrates allows fast growth at minute concentrations of individual substrates. The second strategy is to minimize maintenance requirements (unfortunately we still know little about how this is achieved). Recently, flow cytometry has been employed to study microbial growth in very dilute, nutrient-poor environments. The technique allows fast and easy quantification of microbial growth of natural bacterial communities, including "uncultivable" members, under environmental conditions. When combined with strain-specific fluorescent immunoprobes, this technique allows investigation of the growth and competition of pathogens with the indigenous microbial flora. This method is particularly suited for studying questions concerning microbial growth and survival in drinking water systems.

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low ( approximately 10(2) ppb; approximately 1 muM) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.