Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column.

Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter.

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes.

Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.

Biologically derived fertilizer: A multifaceted bio-tool in methane mitigation.

Methane emissions are affected by agricultural practices. Agriculture has increased in scale and intensity because of greater food, feed and energy demands. The application of chemical fertilizers in agriculture, particularly in paddy fields, has contributed to increased atmospheric methane emissions. Using organic fertilizers may improve crop yields and the methane sink potential within agricultural systems, which may be further improved when combined with beneficial microbes (i.e. biofertilizers) that improve the activity of methane oxidizing bacteria such as methanotrophs. Biofertilizers may be an effective tool for agriculture that is environmentally beneficial compared to conventional inorganic fertilizers. This review highlights and discusses the interplay between ammonia and methane oxidizing bacteria, the potential interactions of microbial communities with microbially-enriched organic amendments and the possible role of these biofertilizers in augmenting the methane sink potential of soils. It is suggested that biofertilizer applications should not only be investigated in terms of sustainable agriculture productivity and environmental management, but also in terms of their effects on methanogen and methanotroph populations.

Methane as a resource: can the methanotrophs add value?

Methane is an abundant gas used in energy recovery systems, heating, and transport. Methanotrophs are bacteria capable of using methane as their sole carbon source. Although intensively researched, the myriad of potential biotechnological applications of methanotrophic bacteria has not been comprehensively discussed in a single review. Methanotrophs can generate single-cell protein, biopolymers, components for nanotechnology applications (surface layers), soluble metabolites (methanol, formaldehyde, organic acids, and ectoine), lipids (biodiesel and health supplements), growth media, and vitamin B12 using methane as their carbon source. They may be genetically engineered to produce new compounds such as carotenoids or farnesene. Some enzymes (dehydrogenases, oxidase, and catalase) are valuable products with high conversion efficiencies and can generate methanol or sequester CO2 as formic acid ex vivo. Live cultures can be used for bioremediation, chemical transformation (propene to propylene oxide), wastewater denitrification, as components of biosensors, or possibly for directly generating electricity. This review demonstrates the potential for methanotrophs and their consortia to generate value while using methane as a carbon source. While there are notable challenges using a low solubility gas as a carbon source, the massive methane resource, and the potential cost savings while sequestering a greenhouse gas, keeps interest piqued in these unique bacteria.

Insight into the effects of biochar on manure composting: evidence supporting the relationship between N2O emission and denitrifying community.

Although nitrous oxide (N2O) emissions from composting contribute to the accelerated greenhouse effect, it is difficult to implement practical methods to mitigate these emissions. In this study, the effects of biochar amendment during pig manure composting were investigated to evaluate the inter-relationships between N2O emission and the abundance of denitrifying bacteria. Analytical results from two pilot composting treatments with (PWSB, pig manure + wood chips + sawdust + biochar) or without (PWS, pig manure + wood chips + sawdust) biochar (3% w/w) demonstrated that biochar amendment not only lowered NO2(-)-N concentrations but also lowered the total N2O emissions from pig manure composting, especially during the later stages. Quantification of functional genes involved in denitrification and Spearman rank correlations matrix revealed that the N2O emission rates correlated with the abundance of nosZ, nirK, and nirS genes. Biochar-amended pig manure had a higher pH and a lower moisture content. Biochar amendment altered the abundance of denitrifying bacteria significantly; less N2O-producing and more N2O-consuming bacteria were present in the PWSB, and this significantly lowered N2O emissions in the maturation phase. Together, the results demonstrate that biochar amendment could be a novel greenhouse gas mitigation strategy during pig manure composting.

Influence of nitrogen limitation on performance of a microbial fuel cell.

We describe the operation of a microbial fuel cell (MFC) system operating on a synthetic wastewater (acetic acid), under conditions of increasing nitrogen limitation. Two MFCs were operated under feed conditions which spanned a range of TKN/COD values of 1.6-28 mg/g. Stable operation was observed in all cases, even when no ammoniacal nitrogen was added to the cell. Improved electrochemical performance (measured as power density, W/m2) was observed as nitrogen limitation was imposed on the cells. Even with no ammonium addition, continuous function of the cell was maintained, at levels consistent with operation at balanced nutrient supplementation. The work has implicated biological nitrogen fixation as a potential source of nitrogen within the MFC. Whilst this hypothesis has yet to be confirmed, the work highlights the opportunity for continuous operation of microbial fuel cells utilising wastewaters with extremely low nitrogen levels, present in pulp and paper, pharmaceutical and petrochemical industries. Further, the described increases in some of the electrochemical indices (e.g. power density) under application of nitrogen limitation may provide a new approach to increasing fuel cell performance. Finally, the lack of any need to add supplemental nitrogen to a MFC-based wastewater treatment technology holds potential for significant financial and environmental savings.

Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum.

Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Data revealed that 91.4% of total ARGs were shared across four root-associated compartments (endosphere, episphere, rhizosphere and unplanted soil). Rather than compartment-selective dynamics of microbiota, the resistome was disseminated in a continuous fashion along the soil-root continuum. Such dissemination was independent of underlying root-associated bacterial and fungal microbiota, but might be facilitated by a multiplicity of mobile genetic elements. As the multiple-drug resistant pathogens, Vibrio vulnificus, pathogenic Escherichia coli and Klebsiella pneumoniae consistently predominated across four compartments, indicating the potential dissemination of antibiotic pathogens along the soil-root continuum. Through deciphering the profile and dynamics of the root-associated resistome and pathogens, our study identified the soil-root continuum as an interconnected sink through which certain ARGs and pathogens can flow from soil into the plant.

Carbon nanotube-grafted chitosan and its adsorption capacity for phenol in aqueous solution.

Chitosan was covalently grafted onto the surface of multi-walled carbon nanotubes to create a novel chitosan/multi-walled carbon nanotube. The structure of the new material was characterized using Fourier transform-infrared spectroscopy, cross polarization magic angle spinning 13C nuclear magnetic resonance, thermogravimetric analysis, XRD ray diffraction analysis, differential scanning calorimetry and scanning electron microscopy. The phenol adsorption capacity was determined and the Langmuir and Freundlich models were used to describe the adsorption isotherms. The adsorption capacity of the novel chitosan/multi-walled carbon nanotube material for phenol (86.96 mg/g) was improved compared to the original chitosan (61.69 mg/g). The kinetic studies showed rapid adsorption, exhibiting Lagergren second-order kinetics. Therefore, this study provides a reference for preparing functional materials from biological substrates that are able to remove toxic pollutants from an aqueous environment.

Effects of metal ions and pH on ofloxacin sorption to cassava residue-derived biochar.

In this study, the impacts of various cations, cation strength and pH on ofloxacin (OFL) adsorption to cassava residue-derived biochars were determined. The associated adsorption mechanisms are discussed. The biochars were prepared at pyrolysis temperatures ranging from 350°C to 750°C, and labeled as CW350, CW450, CW550, CW650 and CW750. The Freundlich model provided the best fit to describe the adsorption capacity of OFL and the Freundlich coefficient (logKf) increased with increasing pyrolysis temperature. The inclusion of Zn2+ or Al3+ increased OFL sorption capacities of five biochars, while Cu2+ reduced sorption to CW450 and CW550. No significant impacts on OFL sorption were observed in the presence of K+ and Ca2+. The concentration of Ca2+ affected the adsorption capacity of CW550, but had no significant impact on other biochars. The pH of OFL solution, ranging from 3 to 9, had no significant changes on OFL adsorption by all the tested biochars. Results of FTIR spectra and zeta potential indicated that electrostatic interactions, cationic exchange, metal bridging and micropore filling could be the main sorption mechanism between OFL and biochars. These studies indicated that cassava residue can be converted into biochars that are effective adsorbents for removing OFL from aqueous solution.

Bioremediation of a wine distillery wastewater using white rot fungi and the subsequent production of laccase.

The aim of this work was to ascertain whether a submerged culture of a white rot fungus could be used to treat distillery wastewater, and whether the compounds present in the wastewater would stimulate laccase production. Trametes pubescens MB 89, Ceriporiopsis subvermispora, Pycnoporus cinnabarinus and UD4 were screened for their ability for the bioremediation of a raw, untreated distillery wastewater as well as distillery wastewater that had been pretreated by polyvinylpolypyrrolidone. Suitability of each strain was measured as a function of decreasing the chemical oxygen demand (COD) and total phenolic compounds concentration and the colour of the wastewater, while simultaneously producing laccase in high titres. After screening, T. pubescens MB 89 was used further in flask cultures and attained 79 +/- 1.1% COD removal, 80 +/- 4.6% total phenols removal, 71 +/- 1.6% decrease in colour at an absorbance of 500 nm and increased the pH from 5.3 to near-neutral. Laccase activity in flask cultures peaked at 4,644 +/- 228 units/l, while the activity in a 50 l bubble lift reactor peaked at 12,966 +/- 71 units/l. Trametes pubescens MB 89 greatly improved the quality of a wastewater known for toxicity towards biological treatment systems, while simultaneously producing an industrially relevant enzyme.

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.

BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. RESULTS: Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time. CONCLUSIONS: The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.

A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation.

Methane, a carbon source for methanotrophic bacteria, is the principal component of natural gas and is produced during anaerobic digestion of organic matter (biogas). Methanotrophs are a viable source of single cell protein (feed supplement) and can produce various products, since they accumulate osmolytes (e.g. ectoine, sucrose), phospholipids (potential biofuels) and biopolymers (polyhydroxybutyrate, glycogen), among others. Other cell components, such as surface layers, metal chelating proteins (methanobactin), enzymes (methane monooxygenase) or heterologous proteins hold promise as future products. Here, scenarios are presented where ectoine, polyhydroxybutyrate or protein G are synthesised as the primary product, in conjunction with a variety of ancillary products that could enhance process viability. Single or dual-stage processes and volumetric requirements for bioreactors are discussed, in terms of an annual biomass output of 1000 tonnesyear(-1). Product yields are discussed in relation to methane and oxygen consumption and organic waste generation.

Antibiotic-resistant genes and antibiotic-resistant bacteria in the effluent of urban residential areas, hospitals, and a municipal wastewater treatment plant system.

In this study, we determined the abundance of 8 antibiotics (3 tetracyclines, 4 sulfonamides, and 1 trimethoprim), 12 antibiotic-resistant genes (10 tet, 2 sul), 4 antibiotic-resistant bacteria (tetracycline, sulfamethoxazole, and combined resistance), and class 1 integron integrase gene (intI1) in the effluent of residential areas, hospitals, and municipal wastewater treatment plant (WWTP) systems. The concentrations of total/individual targets (antibiotics, genes, and bacteria) varied remarkably among different samples, but the hospital samples generally had a lower abundance than the residential area samples. The WWTP demonstrated removal efficiencies of 50.8% tetracyclines, 66.8% sulfonamides, 0.5 logs to 2.5 logs tet genes, and less than 1 log of sul and intI1 genes, as well as 0.5 log to 1 log removal for target bacteria. Except for the total tetracycline concentration and the proportion of tetracycline-resistant bacteria (R (2) = 0.330, P < 0.05), there was no significant correlation between antibiotics and the corresponding resistant bacteria (P > 0.05). In contrast, various relationships were identified between antibiotics and antibiotic resistance genes (P < 0.05). Tet (A) and tet (B) displayed noticeable relationships with both tetracycline and combined antibiotic-resistant bacteria (P < 0.01).

Fluctuation of dissolved heavy metal concentrations in the leachate from anaerobic digestion of municipal solid waste in commercial scale landfill bioreactors: The effect of pH and associated mechanisms.

Heavy metals present in landfill leachate have infrequently been related to complete anaerobic degradation municipal solid waste (MSW) due to discrete ages of deposited MSW layers and leachate channelling in landfills. In this study, anaerobic digestion of MSW was performed in two enclosed 1000 tonne bioreactors using a unique flood and drain process. Leachates were characterised in terms of pH, soluble chemical oxygen demand, volatile fatty acids (VFAs), ammonium nitrogen and heavy metals over the entire course of digestion. All parameters, including pH, fluctuated during acidogenesis, acetogenesis and methanogenesis, which strongly impacted on the dynamics of dissolved heavy metal concentrations. The simulation of dissolution and precipitation processes indicated that metal sulphide precipitation was not a factor as metal concentrations exceeded solubility limits. The correlation of pH and dissolved heavy metal concentrations indicated that other, mechanisms were involved in the homogenised conditions within the bioreactors. Beside dissolution and precipitation, the main processes most likely involved in metal distributions were adsorption (Zn, Cu, Ni, Pb and Cd), complexation (Cr) or combinations of both process (As and Co).

In situ remediation technologies for mercury-contaminated soil.

Mercury from anthropogenic activities is a pollutant that poses significant risks to humans and the environment. In soils, mercury remediation can be technically challenging and costly, depending on the subsurface mercury distribution, the types of mercury species, and the regulatory requirements. This paper introduces the chemistry of mercury and its implications for in situ mercury remediation, which is followed by a detailed discussion of several in situ Hg remediation technologies in terms of applicability, cost, advantages, and disadvantages. The effect of Hg speciation on remediation performance, as well as Hg transformation during different remediation processes, was detailed. Thermal desorption, electrokinetic, and soil flushing/washing treatments are removal technologies that mobilize and capture insoluble Hg species, while containment, solidification/stabilization, and vitrification immobilize Hg by converting it to less soluble forms. Two emerging technologies, phytoremediation and nanotechnology, are also discussed in this review.

Binding between lead ions and the high-abundance serum proteins.

The interaction between three of the most abundant bovine serum proteins (serum albumin, transferrin and IgG) with Pb(2+) was investigated using electrochemistry. The data was used to construct a new theoretical model of Pb(2+) binding to the high-abundance serum proteins under non-ideal conditions. The binding constants (ß) of Pb(2+) to the individual proteins and a mixture of proteins were measured according to a new theoretical equation (non-ideal state) as well as the McGhee-Von Hippel equation (ideal state). Differences between the models suggested that the ß values obtained using the non-ideal state model was more realistic. Protein-protein interactions and micro-environmental influences affected binding between Pb(2+) and the high-abundance serum proteins. We included a micro-environmental influence factor for the model (Fm), which accurately quantified the effect of micro-environment of the proteome of Pb(2+) binding with the serum proteins. This research provides a useful reference of theoretical and experimental work regarding heavy-metal binding interactions with serum proteins.

Spectroscopic evidence for biochar amendment promoting humic acid synthesis and intensifying humification during composting.

Despite the many benefits of biochar amendment in composting, little information is available about its effects on organic matter humification during the process. In this study the analytical results for two in-vessel composting piles were compared, one amended with biochar (VPSB, pig manure+sawdust+biochar) and the other serving as a control (VPS, pig manure+sawdust). During the 74 days of humification, the increased content of humic acid carbon in VPSB is 16.9% more than that of the control. Spectroscopic analyses show a higher O-alkyl C/alkyl C ratio and aromaticity in VPSB at the thermophilic phase, and peak intensities of fulvic-like and humic-like substances were achieved faster in VPSB than VPS. These data inferred that biochar amendment promoted the neo-synthesis of humic acids and intensified the humification of pig manure. Increase in carboxylic groups of biochar as a result of oxidation reactions and sorption of humic substances may correspond to the faster formation of aromatic polymers in biochar-supplemented composting pile. The results suggest that biochar amendment might be a potential method to enhance humification during pig manure composting.

Thermal and thermo-chemical pre-treatment of four waste residues and the effect on acetic acid production and methane synthesis.

In this study four diverse solid waste substrates (coal, Kraft pulp solids, chicken feathers and chicken processing waste) were thermally pre-treated (70, 140 and 200 °C), under an inert (nitrogen) or oxidative (oxygen) atmosphere, and then anaerobically digested. Membrane inlet mass spectrometry during the thermal and thermo-chemical reactions was successfully used to establish oxygen and carbon dioxide gas fluxes and product formation (acetic acid). There was significant solids hydrolysis pre-treatment at 200 °C under an oxidative atmosphere, as indicated by a decrease in the volatile suspended solids and an increase in dissolved organic carbon. Greater concentrations of volatile fatty acids were produced under oxidative conditions at higher temperatures. The methane yield more than tripled for feathers after pre-treatment at 140 °C (under both atmospheres), but decreased after oxidative pre-treatment at 200 °C, due to the destruction of available carbon by the thermo-chemical reaction. Methane yield more than doubled for the Kraft pulp solids with the 200 °C pre-treatment under oxidative conditions. This study illustrated the power of wet oxidation for solids destruction and its potential to improve methane yields generated during anaerobic digestion.

Improved Laccase Production by Trametes pubescens MB89 in Distillery Wastewaters.

Various culture parameters were optimised for laccase synthesis by Trametes pubescens MB89, including pH, carbon source, nitrogen source, lignocellulosic supplements, and reported inducers. Glucose, in conjunction with a complex nitrogen source at pH 5.0, resulted in the highest laccase yield. Adding ethanol, copper, or 2,5-xylidine prior to inoculation further improved laccase concentrations. The addition of 2,5-xylidine was further investigated with multiple additions applied at varying times. This novel application substantially improved laccase production when applied regularly from inoculation and during the growth phase, and also countered glucose repression of laccase synthesis. Single and multiple factor changes were studied in three distillery wastewaters and a wine lees. A synergistic increase in laccase synthesis was observed with the addition of glucose, copper, and 2,5-xylidine. Single addition of 2,5-xylidine proved most beneficial with distillery wastewaters, while copper addition was most beneficial when using the wine lees as a culture medium.