A biogeochemical framework for metal detoxification in sulfidic systems

We develop a comprehensive biogeochemical framework for understanding and quantitatively evaluating metals bio-protection in sulfidic microbial systems. We implement the biogeochemical framework in CCBATCH by expanding its chemical equilibrium and biological sub-models for surface complexation and the formation of soluble and solid products, respectively. We apply the expanded CCBATCH to understand the relative importance of the various key ligands of sulfidic systems in Zn detoxification. Our biogeochemical analysis emphasizes the relative importance of sulfide over other microbial products in Zn detoxification, because the sulfide yield is an order of magnitude higher than that of other microbial products, while its reactivity toward metals also is highest. In particular, metal-titration simulations using the expanded CCBATCH in a batch mode illustrate how sulfide detoxifies Zn, controlling its speciation as long as total sulfide is greater than added Zn. Only in the absence of sulfide does complexation of Zn to biogenic organic ligands play a role in detoxification. Our biogeochemical analysis conveys fundamental insight on the potential of the key ligands of sulfidic systems to effect Zn detoxification. Sulfide stands out for its reactivity and prevalence in sulfidic systems.     

Toxicity and bioremediation of As(III) and As(V) in the green microalgae Botryococcus braunii: A laboratory study

Worldwide threats of fuel shortages in the near future and climate change because of greenhouse gas emissions are posing severe challenges and therefore it is vital to search for sustainable ways of preventing the consequences. The dual use of microalgae for phycoremediation and biomass production for sustainable biofuel production is a viable choice. Phycoremediation of As(III) and As(V) ions using microalgae was investigated in a two-staged batch reactor. Accumulation and toxicity of inorganic arsenic forms (As(III) and As(V)) to green microalgae Botryococcus braunii depend on environmental factors. Dissolved oxygen and pH cycles did not significantly differ due to the absence or presence of arsenic (either As(III) or As(V)) ions in the culture. Monod model was utilized for representing the growth kinetics of microalgae in pure media containing various concentrations of nitrate ions. Maximum specific growth rate and saturation constant were found to be 0.14788 d^?1 and 0.00105 g/L, respectively. With the increase in concentration of phosphate in growth medium, the growth of microalgae increased. Media with NaCl (1.0 g/L) and NaHCO₃ (1 g/L) resulted in higher maximum biomass concentration. Effect of coexisting ions on phycoremediation of As(III) and As(V) ions using microalgae was studied.     

Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation

The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)-bioreduction and achieves detoxification of organic/inorganic contaminants. Although, much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage-host interactions and virus community dynamics in these environments. The objective was to determine the responses of soil bacterial communities and viral assemblages to stimulated anaerobic Fe(III)-bioreduction following electron donor (e.g. acetate) addition. Microbial communities, including viral assemblages, were investigated after 60 days of Fe(III)-bioreduction in laboratory-scale columns continuously fed with acetate-amended artificial groundwater. Viral abundances were greatest in the influent section and decreased along the flow path. Acetate availability was important in influencing bacterial diversity, microbial interactions and viral abundance and community composition. The impact of acetate addition was most evident in the influent section of the columns. The increased relative abundance of Fe(III)-reducing bacteria coincided with an increase in viral abundance in areas of the columns exhibiting the most Fe(III) reduction. The genetic composition of viruses in these column sections also differed from the control column and distal sections of acetate-treated columns suggesting viral communities responded to biostimulated Fe(III)-bioreduction.     

A framework for how environment contributes to cancer risk

Evolutionary theory explains why metazoan species are largely protected against the negative fitness effects of cancers. Nevertheless, cancer is often observed at high incidence across a range of species. Although there are many challenges to quantifying cancer epidemiology and assessing its causes, we claim that most modern‐day cancer in animals – and humans in particular – are due to environments deviating from central tendencies of distributions that have prevailed during cancer resistance evolution. Such novel environmental conditions may be natural and/or of anthropogenic origin, and may interface with cancer risk in numerous ways, broadly classifiable as those: increasing organism body size and/or life span, disrupting processes within the organism, and affecting germline. We argue that anthropogenic influences, in particular, explain much of the present‐day cancer risk across life, including in humans. Based on a literature survey of animal species and a parameterised mathematical model for humans, we suggest that combined risks of all cancers in a population beyond c. 5% can be explained to some extent by the influence of novel environments. Our framework provides a basis for understanding how natural environmental variation and human activity impact cancer risk, with potential implications for species ecology.     

Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon

The demand for petroleum and petroleum products is increasing day by day, while oil spills and improper discharge of industrial wastes contributes to the rising contamination of the environment with petroleum hydrocarbon. Petroleum hydrocarbon spills cause various carcinogenic and neurotoxic effects, and thus effective treatment strategies are required. The various physical and chemical methods currently in use are costly and leave toxic residues in the environment. In contrast, bioremediation is a promising technology in the treatment of petroleum hydrocarbon contamination because of its high effectiveness, lower cost and environmental synergy. Here, we review the biodegradation of petroleum hydrocarbon and various factors influencing this process.     

Development of a sensitivity analysis framework for aquatic biogeochemical models using machine learning

Our evolving understanding of ecosystem functioning along with the advent of computational power have paved the way for the development of complex mathematical models that explicitly represent the functional diversity of biotic communities and multiple biogeochemical cycles. The ever-growing demand for more complex models underscores the importance of robust sensitivity analysis (SA) to elucidate the impact of the uncertainty on model inputs and to untangle the parameter covariance patterns that ultimately lead to the emergence of equifinality problems. In this study, we propose a novel multi-pronged SA framework that integrates advanced statistical and machine learning (ML) techniques. Principal component analysis (PCA) is first applied to dissect the wide array of predictive outputs and identify modes of variability in time and/or space. Classification and Regression Tree (CART) analysis is then used to identify a set of splitting decisions connecting threshold values of key state variables and model parameters with different ranges of predictive outputs with management interest. Self-Organizing Maps (SOM) are implemented as a final step to unravel any non-linear associations between model parameters and responses. As a proof-of-concept, we used a complex aquatic biogeochemical model developed for the Bay of Quinte, a eutrophic embayment in Lake Ontario, to examine competition patterns and structural shifts among multiple functional phytoplankton (diatoms, N-fixing cyanobacteria, and Microcystis) and zooplankton (herbivores and omnivores) groups. Our sensitivity analysis framework showed that the parameters representing the dependence of growth and metabolic processes on temperature are particularly influential to recreate plankton community dynamics during the cold period of the year, whereas the interplay among the interspecific resource competition, strength of the prey-predator interactions, and phosphorus availability mainly regulate their dynamics during the growing season. The growth strategies of diatoms, their nutritional quality that determines the assimilation efficiency by zooplankton, along with the ambient nutrient availability determine our capacity to reproduce patterns of cyanobacteria dominance and faithfully depict the severity of harmful algal blooms. Finally, our study discusses the benefits of a broader use of the ML-based SA framework to unravel influential parametric interactions in modulating the behaviors of complex mathematical models.     

Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants

This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.     

The role of interface framework residues in determining antibody V(H)/V(L) interaction strength and antigen-binding affinity

While many antibodies with strong antigen-binding affinity have stable variable regions with a strong antibody heavy chain variable region fragment (V(H))/antibody light chain variable region fragment (V(L)) interaction, the anti-lysozyme IgG HyHEL-10 has a fairly strong affinity, yet a very weak V(H)/V(L) interaction strength, in the absence of antigen. To investigate the possible relationship between antigen-binding affinity and V(H)/V(L) interaction strength, a novel phage display system that can switch two display modes was employed. We focused on the two framework region 2 regions of the HyHEL-10 V(H) and V(L), facing each other at the domain interface, and a combinatorial library was made in which each framework region 2 residue was mixed with that of D1.3, which has a far stronger V(H)/V(L) interaction. The phagemid library, encoding V(H) gene 7 and V(L) amber codon gene 9, was used to transform TG-1 (sup+), and the phages displaying functional variable regions were selected. The selected phages were then used to infect a nonsuppressing strain, and the culture supernatant containing V(H)-displaying phages and soluble V(L) fragment was used to evaluate the V(H)/V(L) interaction strength. The results clearly showed the existence of a key framework region 2 residue (H39) that strongly affects V(H)/V(L) interaction strength, and a marked positive correlation between the antigen-binding affinity and the V(H)/V(L) interaction, especially in the presence of a set of particular V(L) residues. The effect of the H39 mutation on the wild-type variable region was also confirmed by a SPR biosensor as a several-fold increase in antigen-binding affinity owing to an increased association rate, while a slight decrease was observed for the single-chain variable region.     

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re‐construct high‐quality draft genomes from complex samples. We applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla with no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin–Benson–Bassham, Wood–Ljungdahl or 3‐hydroxyproprionate/4‐hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium‐oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. This organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.     

Potential use of organomineral complex (OMC) for bioremediation of pentachlorophenol (PCP) in soil

Adsorption/desorption characteristics for the organic pollutant pentachlorophenol (PCP) were determined for the organomineral complex (OMC) prepared in the laboratory with clay mineral (zeolite–clinoptilolite) and organic matter (humic acids), both natural products with excellent sorption properties. Sorption experiments were carried out in three characterized soil samples, Calcaro-haplic Chernozem, Gleyic Fluvisol, and Arenic Regosol. The results of this study indicate that OMC has better retention abilities than the clay minerals alone. Higher amounts of humic acids (HAs), bound to zeolite, enhance its potential to adsorb and retain PCP. An OMC containing approx. 5 mg HA g⁻¹ of zeolite possessed the best retention ability for PCP and presented an optimal economic solution from the preparation point of view. Then biodegradation of PCP was studied in the same types of sterilized soils bioaugmented with the bacterial isolate Comamonas testosteroni CCM 7350, with and without the addition of OMC. The immobilization effect of OMC in relation to PCP depends on the concentration of PCP and the content of organic carbon in the soil. The activity of the microorganisms and the effect of acid rain led to the gradual release and biodegradation of the irreversibly bound PCP, without any initial toxic effect on indigenous or bioaugmented microorganisms. OMC appeared to be a good adsorbant for PCP, with potential application in remediation technology. Fast and effective adsorption and low desorption may serve as a pretreatment step for bioremediation technology for reducing PCP content in soil and thus for reducing its potential toxicity, reducing bioavailability, and in this way facilitating biodegradation.     

Enrichment of anammox bacteria from marine environment for the construction of a bioremediation reactor

In the global ocean nitrogen cycle, the anaerobic ammonium-oxidizing (anammox) process is recognized as important. In this study, we established an enrichment culture of marine anammox bacteria (MAB) in a column-type reactor. The reactor, which included a porous polyester non-woven fabric that had been placed at the sea floor in advance for enrichment, was continuously fed with NH₄Cl and NaNO₂ for more than 1 year. Anammox activity in the MAB reactor was confirmed by ¹⁵N tracer analysis using ¹⁵NH₄Cl and Na¹⁴NO₂. We identified two 16S rRNA genes in the amplified DNA fragments derived from MAB, which were highly homologous with those from Candidatus “Scalindua wagneri” and an uncultured planctomycete clone. Fluorescence in situ hybridization analysis using an anammox-specific probe also confirmed that MAB predominated in the reactor. To our knowledge, this is the first report on the establishment of an enrichment culture of anammox bacteria from the marine environment using a continuous culture system.     

A molecular framework for the phylogeny of the Pseudocerotidae (Platyhelminthes,Polycladida)

Systematic relationships within the cotylean family Pseudocerotidae were examined using nucleotide sequences of the D3 expansion segment of the 28S rDNA gene. A previously suggested separation of Pseudoceros and Pseudobiceros based on the number of male reproductive systems was confirmed. Regardless of the algorithm employed, Pseudoceros always formed a monophyletic clade. Pseudobiceros appeared to be paraphyletic; however, a constrained maximum parsimony tree was not significantly longer (2 steps, = 0.05). Additionally, the genera Maiazoon, Phrikoceros and Tytthosoceros were validated as taxonomic entities, and their relationships to other genera within the family were determined. Molecular data also supported species separations based on colour patterns. An intraspecific genetic distance of 1.14% was found for Pseudoceros bifurcus, whereas the intrageneric distance was 3.58%. Genetic distances among genera varied, with the closest distance being 2.048% between Pseudobiceros and Maiazoon, and the largest distance (8.345%) between Pseudoceros and Tytthosoceros.     

2020污染土壤的生物修复专刊序言

生物修复技术,作为可持续发展的重要方向,因其环境友好、高效且无二次污染并能从根本上解决土壤污染问题而受到关注,已经在土壤污染治理中得到了广泛的应用。为了梳理和凝练生物修复技术的发展状况,本专刊收录了该研究领域的16篇论文,分别从植物修复、微生物修复、联合修复、重金属吸收积累的相关分子机制、资源化再利用等方面,详细阐述生物修复技术的发展动态,展望未来的发展趋势,为促进生物修复技术的发展提供参考。     

A molecular phylogenetic framework for the subfamily Ocenebrinae (Gastropoda,Muricidae)

The Ocenebrinae is a subfamily of marine predatory gastropods known as oyster and mussel drills. Their current phylogenetic framework is traditionally based on shell and radular characters, but a consensus on relationships among genera is still lacking. We investigated the molecular phylogeny of Ocenebrinae using 50 species and DNA data from one nuclear (28S) and two mitochondrial (COI and 16S) genes, the largest data set so far assembled for this subfamily. We found support for the monophyly of the Ocenebrinae, and species were divided into four major lineages. Within groups, genera had similar geographic distributions, suggesting that except in a few cases, species diversification within clades occurred without range expansions. We discuss the phylogenetic distribution of a labral tooth and a sealed siphonal canal, two characteristic ocenebrine features. We also show that Ocinebrina species in the north‐eastern Pacific are not monophyletic with north‐eastern Atlantic and Mediterranean species, and that the Ocinebrina edwardsii species complex belongs to Ocenebra.     

Human placenta type V collagens. Evidence for the existence of an alpha 1(V) alpha 2(V) alpha 3(V) collagen molecule

Human type V collagen was purified from placenta and found to contain alpha 1(V), alpha 2(V), and alpha 3(V) chains in varying ratios. Using any of three independent nondenaturing methods (phosphocellulose chromatography, high-performance ion-exchange chromatography on IEX-540 DEAE, and ammonium sulfate precipitation), this preparation could be resolved into two fractions. Analysis of the two fractions by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that one fraction contained alpha 1(V) and alpha 2(V) in a 2:1 ratio and the other contained alpha 1(V), alpha 2(V), and alpha 3(V) in a 1:1:1 ratio. When the crude placental type V collagen was electrophoresed under nondenaturing conditions, two bands were observed, one co-migrating with purified (alpha 1(V]2 alpha 2(V) and the other co-migrating with the fractions containing alpha 1(V), alpha 2(V), and alpha 3(V) chains in a 1:1:1 ratio. Electrophoresis in a second dimension under denaturing conditions confirmed that the fast-migrating band contained (alpha 1(V]2 alpha 2(V) and that the slow-migrating band contained the three chains in equimolar ratio. CD spectra of the two fractions and resistance to trypsin-chymotrypsin digestion confirmed that the two fractions contain triple helical collagen. Thermal denaturations were monitored by the changes in CD signal at 221 nm. The two fractions purified by ammonium sulfate precipitation melted at 39.1 and 36.4 degrees C for the (alpha 1(V]2 alpha 2(V) and alpha 1(V) alpha 2(V) alpha 3(V) fractions, respectively. Trypsin cleavage of these two native fractions at temperatures near melting produced completely different fragmentation patterns, indicating different partial unwinding sites of the alpha 1(V) and alpha 2(V) chains in the two preparations and thus different molecular assemblies. Our data demonstrate the existence of two different molecular assemblies of type V collagen in human placenta consisting of (alpha 1(V]2 alpha 2(V) and alpha 1(V) alpha 2(V) alpha 3(V) heterotrimers.