Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated naval sites

Degradation and habitat-dependent colonization of plastics in Caribbean coastal waters and sediments by bacterial communities

This study investigates microbial colonization of plastics in Caribbean coastal waters. We deployed five polymer types, on set with a mild UV-pretreatment and one set without UV-pretreatment, for 4.5 months in the water column and sediment at two locations, and analyzed the epiplastic biofilms with 16S rRNA gene sequencing. While a significant influence of location and habitat was apparent, we could not detect notable effects related to polymer type or UV-pretreatment on microbial community composition. Nevertheless, potential plastic and hydrocarbon degraders constituted up to 43 % of sequences from epiplastic biofilms, suggesting an affinity for plastic. Indeed, utilizing 13C-labeled PE and PP, we determined incorporation of plastic-derived carbon into microbial biomass. We measured isotopically labeled fatty acids in incubations with 13C labeled plastics in both water column and sediments, whether virgin or pre-weathered with UV light. The apparent biodegradation of plastic in benthic habitats challenges the perception of marine sediments as a final sink for polyolefins.

Soil Bacterial Community Characteristics and Functional Analysis of Estuarine Wetlands and Nearshore Estuarine Wetlands in Qinghai Lake

Qinghai Lake, the largest inland saline lake in China, plays a vital role in wetland carbon cycling. However, the structure and function of soil bacterial communities in its estuarine and nearshore estuarine wetlands remain unclear. This study examined the effects of wetland type and soil depth on bacterial diversity, community composition, and functional potential in the Shaliu, Heima, and Daotang River wetlands using high-throughput sequencing. The results showed that wetland type and soil depth significantly influenced bacterial communities. Nearshore wetlands exhibited lower bacterial diversity in the 0-10 cm layer, while deeper soils (10-20 cm) showed greater regional differentiation. Estuarine wetlands were enriched with Proteobacteria, Actinobacteriota, and Chloroflexi, whereas nearshore wetlands were dominated by Actinobacteriota and Cyanobacteria. Functionally, estuarine wetlands had higher sulfate reduction and anaerobic decomposition potential, with Desulfovibrio, Desulfobacter, and Desulfotomaculum regulating sulfur cycling and carbon decomposition. In contrast, nearshore wetlands showed greater nitrogen fixation and organic matter degradation, facilitated by Rhizobium, Azotobacter, Clostridium, and nitrogen-fixing Cyanobacteria (e.g., Anabaena, Nostoc). Microbial metabolic functions varied by depth: surface soils (0-10 cm) favored environmental adaptation and organic degradation, whereas deeper soils (10-20 cm) exhibited lipid metabolism and DNA repair strategies for low-oxygen adaptation. These findings highlight the spatial heterogeneity of bacterial communities and their role in biogeochemical cycles, providing insights into wetland carbon dynamics and informing conservation strategies.

Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize

Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.

Isolation, identification and transcriptome analysis of triadimefon-degrading strain Enterobacter hormaechei TY18

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon-nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully.

An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase

Soil and groundwater were investigated for the genes encoding soluble and particulate methane monooxygenase/ammonia monooxygenase (sMMO, pMMO/AMO), toluene 4-monooxygenase (T4MO), propane monooxygenase (PMO) and phenol hydroxylase (PH). The objectives were (1) to determine which subunits were present, (2) to examine the diversity of the phylotypes associated with the biomarkers and (3) to identify which metagenome associated genomes (MAGs) contained these subunits. All T4MO and PH subunits were annotated in the groundwater metagenomes, while few were annotated in the soil metagenomes. The majority of the soil metagenomes included only four sMMO subunits. Only two groundwater metagenomes contained five sMMO subunits. Gene counts for the pMMO subunits varied between samples. The majority of the soil metagenomes were annotated for all four PMO subunits, while three out of eight groundwater metagenomes contained all four PMO subunits. A comparison of the blast alignments for the sMMO alpha chain (mmoX) indicated the phylotypes differed between the soil and groundwater metagenomes. For the pMMO/AMO alpha subunit (pmoA/amoA), Nitrosospira was important for the soil metagenomes, while Methylosinus and Methylocystis were dominant for the groundwater metagenomes. The majority of pmoA alignments from both metagenomes were from uncultured bacteria. High quality MAGs were obtained from the groundwater data. Four MAGs (Methylocella and Cypionkella) contained sMMO subunits. Another three MAGs, within the order Pseudomonadales, contained all three pMMO subunits. All PH subunits were detected in seven MAGs (Azonexus, Rhodoferax, Aquabacterium). In those seven, all contained catechol 2,3-dioxagenase, and Aquabacterium also contained catechol 1,2-dioxygenase. T4MO subunits were detected in eight MAGs (Azonexus, Rhodoferax, Siculibacillus) and all, except one, contained all six subunits. Four MAGs (Rhodoferax and Azonexus) contained all subunits for PH and T4MO, as well as catechol 2,3-dixoygenase. The detection of T4MO and PH in groundwater metagenomes and MAGs has important implications for the potential oxidation of groundwater contaminants.

Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp

BACKGROUND

Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathogens. However, the mechanisms of how low salinity stress induces disease susceptibility remain poorly understood.

METHODS

We investigated the acute response of shrimp gut microbiota exposed to pathogens under low salinity stress. For comparison, shrimp were exposed to Vibrio infection under two salinity conditions: optimal salinity (Control group) and low salinity stress (Stress group). High throughput 16S rRNA sequencing and real-time PCR were employed to characterize the shrimp gut microbiota and quantify the severity level of Vibrio infection.

RESULTS

The results showed that low salinity stress increased Vibrio infection levels, reduced gut microbiota species richness, and perturbed microbial functions in the shrimp gut, leading to significant changes in lipopolysaccharide biosynthesis that promoted the growth of pathogens. Gut microbiota of the bacterial genera Candidatus Bacilliplasma, Cellvibrio, and Photobacterium were identified as biomarkers of the Stress group. The functions of the gut microbiota in the Stress group were primarily associated with cellular processes and the metabolism of lipid-related compounds.

CONCLUSIONS

Our findings reveal how environmental stress, particularly low salinity, increases shrimp susceptibility to Vibrio infection by affecting the gut microbiota. This highlights the importance of avoiding low salinity stress and promoting gut microbiota resilience to maintain the health of shrimp.

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Screening of hazardous groundwater pollutants responsible for microbial ecological consequences by integrated nontargeted analysis and high-throughput sequencing technologies

Organic contaminants, especially hydrophobic organic contaminants (HOCs), pose potential ecological threats even at environmental concentrations. Characterization of HOC profiles and identification of key environmental stressors are vital but still challenging in groundwater quality management. In this study, a strategy for identifying the key environmental stressors among HOCs in groundwater based on integrated chemical monitoring technologies and microbial ecology analysis methods was proposed and applied to typical groundwater samples. Specifically, the characteristics of HOCs were systematically analyzed based on nontargeted and targeted approaches, and microbial community assembly and specific biomarker analysis were combined to determine the major ecological processes and key environmental stressors. The results showed that a total of 234 HOCs were detected in groundwater collected from Tongzhou, Beijing; among them, phthalate esters (PAEs) were screened out as key environmental stressors, considering that they made relatively higher microbial ecology contributions. Furthermore, their influences on the structure and function of the groundwater microbial community were evaluated by adopting high-throughput sequencing and bioinformatics analysis technologies. These findings confirmed PAEs as vital determinants driving microbial assembly, shifting community structure, and regulating community function in groundwater; in addition, the findings validated the feasibility and suitability of the proposed strategy.

Temporal, compositional, and functional differences in the microbiome of Bangkok subway air environment

With the growing numbers of the urban population, an increasing number of commuters have relied on subway systems for rapid transportation in daily life. Analyzing the temporal distribution of air microbiomes in subway environments is crucial for the assessment and monitoring of air quality in the subway system, especially with regard to public health. This study employed culture-independent metabarcode sequencing to analyze bacterial diversity and variations in bacterial compositions associated with bioaerosols collected from a subway station in Bangkok over a four-month period. The bacteria obtained were found to consist primarily of Proteobacteria, Firmicutes, and Actinobacteria, with variations at the family, genus, and species levels among samples obtained in different months. The vast majority of these bacteria are most likely derived from outside environments and human body sources. Many of the bacteria found in Bangkok subway station were also identified as "core microorganisms" of subway environments around the world, as suggested by the MetaSUB Consortium. The diversity of bacterial communities was shown to be influenced by several air quality variables, especially ambient temperature and the quantity of particulate matters, which showed positive correlations with several bacterial species such as Acinetobacter lwoffii, Staphylococcus spp., and Moraxella osloensis. In addition, metabolic profiles inferred from metabarcode-derived bacterial diversity showed significant variations across different sampling times and sites and can be used as a starting point to further explore the functional roles of specific groups of bacteria in the subway environment. This study thus introduced the information required for surveillance of microbiological impacts and their contributions to the well-being of subway commuters in Bangkok.

Synergistic PAH biodegradation by a mixed bacterial consortium: based on a multi-substrate enrichment approach

Polycyclic aromatic hydrocarbon (PAH) contamination in the environment involves multiple PAHs and various intermediates produced during the microbial metabolic process. A multi-substrate enrichment approach was proposed to develop a mixed bacterial community (MBC) from the activated sludge of a coking wastewater plant. The degradation performance of MBC was evaluated under different initial concentrations of PAHs (25-200 mg/L), temperature (20-35 °C), pH (5.0-9.0), salinity (0-10 g/L NaCl), and coexisting substrates (catechol, salicylic acid, and phthalic acid). The results showed that the degradation rates of phenanthrene and pyrene in all treatments were up to (99 ± 0.71)% and (99 ± 0.90)% after incubation of 5 days, respectively, indicating excellent biodegradation ability of PAHs by MBC. Furthermore, 16S rRNA gene amplicon sequencing analysis revealed that Pseudomonas was dominant, while Burkholderia had the largest proportion in acidic (pH = 5.0) and saline (10 g/L NaCl) environments. However, the proportion of dominant bacteria in MBC was markedly affected by intermediate metabolites. It was shown that MBC had a higher degradation rate of PAHs in the coexisting matrix due to the timely clearance of intermediates reducing the metabolic burden. Overall, our study provided valuable information to help design an effective strategy for the bioremediation of PAHs in complex environments.

Changes in gut microbial community upon chronic kidney disease

With the increasing incidence and mortality of chronic kidney disease (CKD), targeted therapies for CKD have been explored constantly. The important role of gut microbiota on CKD has been emphasized increasingly, it is necessary to analyze the metabolic mechanism of CKD patients from the perspective of gut microbiota. In this study, bioinformatics was used to analyze the changes of gut microbiota between CKD and healthy control (HC) groups using 315 samples from NCBI database. Diversity analysis showed significant changes in evenness compared to the HC group. PCoA analysis revealed significant differences between the two groups at phylum level. In addition, the F/B ratio was higher in CKD group than in HC group, suggesting the disorder of gut microbiota, imbalance of energy absorption and the occurrence of metabolic syndrome in CKD group. The study found that compared with HC group, the abundance of bacteria associated with impaired kidney was increased in CKD group, such as Ralstonia and Porphyromonas, which were negatively associated with eGFR. PICRUSt2 was used to predict related functions and found that different pathways between the two groups were mainly related to metabolism, involving the metabolism of exogenous and endogenous substances, as well as Glycerophospholipid metabolism, which provided evidence for exploring the relationship between gut microbiota and lipid metabolism. Therefore, in subsequent studies, special attention should be paid to these bacteria and metabolic pathway, and animal experiments and metabolomics studies should be conducted explore the association between bacterial community and CKD, as well as the therapeutic effects of these microbial populations on CKD.

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures

The microbiome of water springs is gaining increasing interest, especially in water intended for human consumption. However, the knowledge about large-scale patterns in water springs microbiome is still incomplete. The presence of bacteria in water sources used for human consumption is a major concern for health authorities; nonetheless, the standard microbiological quality checks are focused only on pathogenic species and total microbial load. Using 16S rRNA high throughput sequencing, we characterized the microbiome from 38 water springs in Trentino (Northern Italy) for 2 consecutive years in order to gain precious insights on the microbiome composition of these unexplored yet hardly exploited environments. The microbiological studies were integrated with standard measurements of physico-chemical parameters performed by the Provincial Office for Environmental Monitoring in order to highlight some of the dynamics influencing the microbial communities of these waters. We found that alpha diversity showed consistent patterns of variation overtime, and showed a strong positive correlation with the water nitrate concentration and negatively with fixed residue, electrical conductivity, and calcium concentration. Surprisingly, alpha diversity did not show any significant correlation with neither pH nor temperature. We found that despite their remarkable stability, different water springs display different coefficients of variation in alpha diversity, and that springs used for similar purposes showed similar microbiomes. Furthermore, the springs could be grouped according to the number of shared species into three major groups: low, mid, and high number of shared taxa, and those three groups of springs were consistent with the spring usage. Species belonging to the phyla Planctomycetes and Verrucomicrobia were prevalent and at relatively high abundance in springs classified as low number of shared species, whereas the phylum Lentisphaerae and the Candidate Phyla radiation were prevalent at higher abundance in the mineral and potable springs. The present study constitutes an example for standard water spring monitoring integrated with microbial community composition on a regional scale, and provides information which could be useful in the design and application of future water management policies in Trentino.

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Soil microbial ecological effect of shale gas oil-based drilling cuttings pyrolysis residue used as soil covering material

The residue derived from oil-based drilling cutting pyrolysis could be used as paving materials. Some petroleum hydrocarbons remain in the residue after pyrolysis and cause severe environmental pollution. In this study, the soil column leaching experiments were carried out under different leaching amounts, and the vertical migration characteristics of petroleum hydrocarbons in soil and the dynamic response mechanism of microorganisms to petroleum hydrocarbons were analyzed. The result showed that the soil pH value and water content with different leaching amounts did not differ significantly, but the vertical migration ability of each petroleum hydrocarbon component was different. In petroleum hydrocarbon contaminated soil, the relative abundance of Proteobacteria maintained a high level (23.6%-60.7%). At the genus level, the relative abundance of Massilia decreased with the leaching amount increased. According to PICRUSt, Monooxygenase [EC: 1.14.13.-] played a significant role in petroleum hydrocarbon degradation. While Long-chain-fatty-acid-CoA ligase [EC: 6.2.1.3] had the highest relative abundance. By studying the influence of shale gas oil-based drilling cuttings pyrolysis residue on soil physical and chemical properties and soil microorganisms, this work provides scientific ecological assessment for the resource application of pyrolysis residue.

Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis

As one of the most environmentally toxic heavy metals, cadmium (Cd) has attracted the attention of researchers globally. In particular, Guangxi, a province in southwestern China, has been subjected to severe Cd pollution due to geogenic processes and anthropogenic activities. Cd can be accumulated in aquatic animals and transferred to the human body through the food chain, with potential health risks. The aim of the present study was to explore the effects of waterborne Cd exposure (0.5 mg/L and 1.5 mg/L) on the intestinal microbiota of mudsnail, Cipangopaludina cathayensis, which is favored by farmers and consumers in Guangxi. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 segment of the bacterial 16S rRNA gene. Our results indicated that C. cathayensis could tolerate low Cd (0.5 mg/L) stress, while Cd exposure at high doses (1.5 mg/L) exerted considerable effects on microbiota composition. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the mudsnail gut microbiota. The relative abundances of Bacteroidetes increased significantly under high Cd exposure (H14) (p < 0.01), with no significant change in the low Cd exposure (L14) treatment. The dominant genera with significant differences in relative abundance were Pseudomonas, Cloacibacterium, Acinetobacter, Dechloromonas, and Rhodobacter. In addition, Cd exposure could significantly alter the pathways associated with metabolism, cellular processes, environmental information processing, genetic information processing, human diseases, and organismal systems. Notably, compared to the L14 treatment, some disease-related pathways were enriched, while some xenobiotic and organic compound biodegradation and metabolism pathways were significantly inhibited in the H14 group. Overall, Cd exposure profoundly influenced community structure and function of gut microbiota, which may in turn influence C. cathayensis gut homeostasis and health.