Burkholderiales participating in pentachlorophenol biodegradation in iron-reducing paddy soil as identified by stable isotope probing

Iron Plaque: A Shield against Soil Contamination and Key to Sustainable Agriculture

Soils play a dominant role in supporting the survival and growth of crops and they are also extremely important for human health and food safety. At present, the contamination of soil by heavy metals remains a globally concerning environmental issue that needs to be resolved. In the environment, iron plaque, naturally occurring on the root surface of wetland plants, is found to be equipped with an excellent ability at blocking the migration of heavy metals from soils to plants, which can be further developed as an environmentally friendly strategy for soil remediation to ensure food security. Because of its large surface-to-volume porous structure, iron plaque exhibits high binding affinity to heavy metals. Moreover, iron plaque can be seen as a reservoir to store nutrients to support the growth of plants. In this review, the formation process of iron plaque, the ecological role that iron plaque plays in the environment and the interaction between iron plaque, plants and microbes, are summarized.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

Metagenome-Assembled Genomes Reveal Mechanisms of Carbohydrate and Nitrogen Metabolism of Schistosomiasis-Transmitting Vector Biomphalaria Glabrata

Biomphalaria glabrata transmits schistosomiasis mansoni which poses considerable risks to hundreds of thousands of people worldwide, and is widely used as a model organism for studies on the snail-schistosome relationship. Gut microbiota plays important roles in multiple aspects of host including development, metabolism, immunity, and even behavior; however, detailed information on the complete diversity and functional profiles of B. glabrata gut microbiota is still limited. This study is the first to reveal the gut microbiome of B. glabrata based on metagenome-assembled genome (MAG). A total of 28 gut samples spanning diet and age were sequenced and 84 individual microbial genomes with ≥ 70% completeness and ≤ 5% contamination were constructed. Bacteroidota and Proteobacteria were the dominant bacteria in the freshwater snail, unlike terrestrial organisms harboring many species of Firmicutes and Bacteroidota. The microbial consortia in B. glabrata helped in the digestion of complex polysaccharide such as starch, hemicellulose, and chitin for energy supply, and protected the snail from food poisoning and nitrate toxicity. Both microbial community and metabolism of B. glabrata were significantly altered by diet. The polysaccharide-degrading bacterium Chryseobacterium was enriched in the gut of snails fed with high-digestibility protein and high polysaccharide diet (HPHP). Notably, B. glabrata as a mobile repository can escalate biosafety issues regarding transmission of various pathogens such as Acinetobacter nosocomialis and Vibrio parahaemolyticus as well as multiple antibiotic resistance genes in the environment and to other organisms. IMPORTANCE The spread of aquatic gastropod Biomphalaria glabrata, an intermediate host of Schistosoma mansoni, exacerbates the burden of schistosomiasis disease worldwide. This study provides insights into the importance of microbiome for basic biological activities of freshwater snails, and offers a valuable microbial genome resource to fill the gap in the analysis of the snail-microbiota-parasite relationship. The results of this study clarified the reasons for the high adaptability of B. glabrata to diverse environments, and further illustrated the role of B. glabrata in accumulation of antibiotic resistance in the environment and spread of various pathogens. These findings have important implications for further exploration of the control of snail dissemination and schistosomiasis from a microbial perspective.

Synergistic Effect of Soil Organic Matter and Nanoscale Zero-Valent Iron on Biodechlorination

Nanoscale zero-valent iron (nZVI) provides a promising solution for organochlorine (OC)-contaminated soil remediation. However, the interactions among nZVI, soil organic matter (SOM), and indigenous dechlorinating bacteria are intricate, which may result in unascertained effects on the reductive degradation of OCs and merits specific investigation. Herein, we isolated an indigenous dehalogenation bacterium (Burkholderia ambifaria strain L3) from a paddy soil and further investigated the biodechlorination of pentachlorophenol (PCP) with individual and a combination of SOM and nZVI. In comparison with individual-strain L3 treatment, the cotreatment with nZVI or SOM increased the removal efficiency of PCP from 34.4 to 44.3-54.2% after 15 day cultivation. More importantly, a synergistic effect of SOM and nZVI was observed on the PCP removal by strain L3, and the PCP removal efficiency reached up to 75.3-84.5%. Other than the biodegradation through ortho- and meta-substitution under the individual application of SOM or nZVI, PCP was further biodegraded to 2,4,6-trichlorophenol (TCP) through para-substitution by the isolated bacteria with the cotreatment of SOM and nZVI. The main roles of the nZVI-SOM cotreatment in the biodegradation included the SOM-facilitated microbial proliferation, the nZVI-promoted microbial transformation of SOM, and the induced higher electron transport capacity of redox Fe-PCP biocycling. These findings provide a novel insight into the action of nZVI in environmental remediations.

Cloning, overexpression, purification, characterization and structural modelling of a metabolically active Fe2+ dependent 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (CpsA) from Bacillus cereus strain AOA-CPS_1

2,6-Dichloro-p-hydroquinone (DiCHQ) aromatic-ring cleavage by DiCHQ 1,2-dioxygenase (CpsA) is very crucial for complete transformation of pentachlorophenol (PCP) to 2-chloromaleylacetate in Bacillus cereus AOA-CPS_1 (BcAOA). The 978 bp gene (cpsA) was detected and amplified in the genome of BcAOA; cloned, overexpressed and purified to homogeneity. CpsA showed a single ≅36.9 kDa protein band on SDS-PAGE and exhibited optimum activity at 30 °C and pH 9.0. CpsA was stable between 20 °C and 40 °C, and also retained about 90% of its activity at 60 °C for 120 min. The enzyme retained about 90% activity between pH 9.0 and 11.5 and 60% activity at pH 13.0. CpsA was found to be Fe²⁺ dependent as about 90% increased activity was observed in the presence of FeSO₄. CpsA showed apparent v_max, K_m, k_cat and k_cat/K_m of 27.77 ± 0.9 μMs^-1, 0.990 ± 0.03 mM, 4.20 ± 0.04 s^-1 and 4.24 ± 0.03 s^-1 mM^-1, respectively at pH 9.0. Analysis of the reaction products via GC-MS confirmed 2-chloromaleylacetate as the ring-cleavage product. CpsA 3D structure revealed a conserved 2-His-1-carboxylate facial triad motif (His 9, His 244 and Thr 11), with Fe³⁺ at the centre. Findings from this study provide new insights into the involvement of this enzyme in PCP degradation and suggests alternate possible mechanism of ring-cleavage by dioxygenases.

Different fertilization treatments in coal mining-affected soils change bacterial populations and enable soil reclamation

Purpose

Coal mining activities result in large-scale soil degradation and ecosystem imbalances in many countries. Fertilization is an effective way to improve soil fertility and microbial activity. However, the effect of different fertilizers and remediation time on the subsided soil is not clear. The aim of this study is to explore the effects on soil fertility and the bacterial community.

Methods

In this study, we compared three fertilization regimes (inorganic, organic, and combined) applied over a 5-year period for the purpose of rehabilitating subsoil through measurement of soil’s chemical properties and microbial biomass. Bacterial diversity was evaluated in different reclaimed soils via high-throughput 16S rDNA sequencing; 1,938,561 total sequences were obtained.

Results

The results showed that fertilization improved various soil properties, including the concentrations of available phosphorus, available potassium, and alkali-hydrolysable nitrogen, therefore, increasing microbial biomass. A significant increase in soil microbial diversity was observed in fertilized soils compared to the initial conditions. A positive correlation between microbial diversity and soil properties was observed. Regarding an improvement in soil properties and crop yields, the organic fertilizer demonstrated significantly more effectiveness compared to the inorganic fertilizer. Meanwhile, the relative abundance of Proteobacteria, Bacteroidetes, and Verrucomicrobia increased, but the relative abundance of Chloroflexi and Nitrospirae decreased. More specifically, we found that several Proteobacteria subgroups, such as Rhizobiales, Myxococcales, Sphingomonadales, Rhodospirillales, Xanthomonadales, and Burkholderiales, increased after the restoration. Additionally, the composition of the bacterial community in the 5-year groups (M5, O5, and MO5) was similar to the composition of the FS group, and the yield of the maize test crop following the 5-year restoration period was close to the average in China.

Conclusion

This result indicates that soil reclamation via fertilization can contribute to soil recovery over time. Therefore, we concluded that fertilization is an effective strategy for the restoration of soil properties and bacterial communities in mining soil.

Bacterial-mediated biodegradation of pentachlorophenol via electron shuttling

Pentachlorophenol (PCP) degradation by soil indigenous bacteria represents a practical and cost-effective solution. In the present study, bacteria isolated from paddy soil was investigated and the role of electron shuttling (ES) in the PCP degradation process was assessed. Two strains demonstrated the highest PCP degradation of 93.5% and 94.88% in the presence of citrate and were identified using 16S rRNA phylogenetic analysis as Pseudomonas chengduensis and Pseudomonas plecoglossicida, respectively. Both strains showed higher PCP degradation in free form as opposed to a reduced activity in immobilized and respiratory impaired form. The addition of pyruvate resulted in about 80% PCP degradation in 5 days for P. chengduensis, on the other hand, P. plecoglossicida showed the same result under anaerobic conditions whether pyruvate was added or not. Phenazine and the outer membrane c-type cytochrome were reported only for P. chengduensis as opposed to P. plecoglossicida. The results indicate that despite following different approaches in PCP degradation, both strains are useful in PCP clean-up under aerobic and anaerobic conditions and in free direct contact. The degradation is enhanced via ES. This is considered both an effective and feasible technology for in situ clean-up of contaminated sites or on-site bioreactors.

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO₂ emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO₂ production.

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood

Injecting CO₂ into depleted oil reservoirs to extract additional crude oil is a common enhanced oil recovery (CO₂-EOR) technique. However, little is known about how in situ microbial communities may be impacted by CO₂ flooding, or if any permanent microbiological changes occur after flooding has ceased. Formation water was collected from an oil field that was flooded for CO₂-EOR in the 1980s, including samples from areas affected by or outside of the flood region, to determine the impacts of CO₂-EOR on reservoir microbial communities. Archaea, specifically methanogens, were more abundant than bacteria in all samples, while identified bacteria exhibited much greater diversity than the archaea. Microbial communities in CO₂-impacted and non-impacted samples did not significantly differ (ANOSIM: Statistic R = -0.2597, significance = 0.769). However, several low abundance bacteria were found to be significantly associated with the CO₂-affected group; very few of these species are known to metabolize CO₂ or are associated with CO₂-rich habitats. Although this study had limitations, on a broad scale, either the CO₂ flood did not impact the microbial community composition of the target formation, or microbial communities in affected wells may have reverted back to pre-injection conditions over the ca. 40 years since the CO₂-EOR.

Challenges of ligand identification for the second wave of orphan riboswitch candidates

Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn2+, and the metabolites guanidine and PRPP. Such studies also yield useful linkages between the ligands sensed by the riboswitches and numerous biochemical pathways. In the current report, we describe the known characteristics of 30 distinct classes of orphan riboswitch candidates - some of which have remained unsolved for over a decade. We also discuss the prospects for uncovering novel biological insights via focused studies on these RNAs. Lastly, we make recommendations for experimental objectives along the path to finding ligands for these mysterious RNAs.

Remediation of phthalates in river sediment by integrated enhanced bioremediation and electrokinetic process

The objective of this study was to evaluate the feasibility of enhanced bioremediation coupling with electrokinetic process for promoting the growth of intrinsic microorganisms and removing phthalate esters (PAEs) from river sediment by adding an oxygen releasing compound (ORC). Test results are given as follows: Enhanced removal of PAEs was obtained by electrokinetics, through which the electroosmotic flow would render desorption of organic pollutants from sediment particles yielding an increased bioavailability. It was also found that the ORC injected into the sediment compartment not only would alleviate the pH value variation due to acid front and base front, but would be directly utilized as the carbon source and oxygen source for microbial growth resulting in an enhanced degradation of organic pollutants. However, injection of the ORC into the anode compartment could yield a lower degree of microbial growth due to the loss of ORC during the transport by EK. Through the analysis of molecular biotechnology it was found that both addition of an ORC and application of an external electric field can be beneficial to the growth of intrinsic microbial and abundance of microflora. In addition, the sequencing result showed that PAEs could be degraded by the following four strains: Flavobacterium sp., Bacillus sp., Pseudomonas sp., and Rhodococcus sp. The above findings confirm that coupling of enhanced bioremediation and electrokinetic process could be a viable remediation technology to treat PAEs-contaminated river sediment.