nhui Lu

The interactions of composting and biochar and their implications for soil amendment and pollution remediation: a review

Abstract Compost and biochar, used for the remediation of soil, are seen as attractive waste management options for the increasing volume of organic wastes being produced. This paper reviews the interaction of biochar and composting and its implication for soil amendment and pollution remediation. The interaction of biochar and composting affect each other’s properties. Biochar could change the physico-chemical properties, microorganisms, degradation, humification and gas emission of composting, such as the increase of nutrients, cation exchange capacity (CEC), organic matter and microbial activities. The composting could also change the physico-chemical properties and facial functional groups of biochar, such as the improvement of nutrients, CEC, functional groups and organic matter. These changes would potentially improve the efficiency of the biochar and composting for soil amendment and pollution remediation. Based on the above review, this paper also discusses the future research required in this field.

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting.

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; P<0.001), indicating that archaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages.

Assessment of heavy metal contamination in the surrounding soils and surface sediments in Xiawangang River, Qingshuitang District.

Xiawanggang River region is considered to be one of the most polluted areas in China due to its huge amount discharge of pollutants and accumulation for years. As it is one branch of Xiang River and the area downstream is Changsha city, the capital of Hunan Province, the ecological niche of Xiawangang River is very important. The pollution treatment in this area was emphasized in the Twelfth Five-Year Plan of Chinese government for Xiang River Water Environmental Pollution Control. In order to assess the heavy metal pollution and provide the base information in this region for The Twelfth Five-Year Plan, contents and fractions of four heavy metals (Cd, Cu, Pb and Zn) covering both sediments and soils were analyzed to study their contamination state. Three different indexes were applied to assess the pollution extent. The results showed this area was severely polluted by the four heavy metals, and the total concentrations exceeded the Chinese environmental quality standard for soil, grade III, especially for Cd. Moreover, Cd, rated as being in high risk, had a high mobility as its great contents of exchangeable and carbonates fractions in spite of its relative low content. Regression analysis revealed clay could well explain the regression equation for Cd, Cu and Zn while pH and sand could significantly interpret the regression equation for Pb. Moreover, there was a significant correlation between Non-residual fraction and Igeo for all the four metals. Correlation analysis showed four metals maybe had similar pollution sources.

Compound microsatellites in complete Escherichia coli genomes.

Compound microsatellites consisting of two or more repeats in close proximity have been found in eukaryotic genomes. So far such compound microsatellites have not been investigated in any prokaryotic genomes. We have therefore examined compound microsatellites in 22 complete genomes of Escherichia coli, which is one of the ideal model organisms to analyze the nature and evolution of prokaryotic compound microsatellites. Our results indicated that about 1.75–2.85% of all microsatellites could be accounted as compound microsatellites with very low complexity, and most compound microsatellites were composed of very different motifs. Compound microsatellites were significantly overrepresented in all surveyed genomes. These results were dramatically different from those in eukaryotes. We discussed the possible reasons for the observed divergence.

Diversity of two-domain laccase-like multicopper oxidase genes in Streptomyces spp.: identification of genes potentially involved in extracellular activities and lignocellulose degradation during composting of agricultural waste.

ABSTRACT Traditional three-domain fungal and bacterial laccases have been extensively studied for their significance in various biotechnological applications. Growing molecular evidence points to a wide occurrence of more recently recognized two-domain laccase-like multicopper oxidase (LMCO) genes in Streptomyces spp. However, the current knowledge about their ecological role and distribution in natural or artificial ecosystems is insufficient. The aim of this study was to investigate the diversity and composition of Streptomyces two-domain LMCO genes in agricultural waste composting, which will contribute to the understanding of the ecological function of Streptomyces two-domain LMCOs with potential extracellular activity and ligninolytic capacity. A new specific PCR primer pair was designed to target the two conserved copper binding regions of Streptomyces two-domain LMCO genes. The obtained sequences mainly clustered with Streptomyces coelicolor, Streptomyces violaceusniger, and Streptomyces griseus. Gene libraries retrieved from six composting samples revealed high diversity and a rapid succession of Streptomyces two-domain LMCO genes during composting. The obtained sequence types cluster in 8 distinct clades, most of which are homologous with Streptomyces two-domain LMCO genes, but the sequences of clades III and VIII do not match with any reference sequence of known streptomycetes. Both lignocellulose degradation rates and phenol oxidase activity at pH 8.0 in the composting process were found to be positively associated with the abundance of Streptomyces two-domain LMCO genes. These observations provide important clues that Streptomyces two-domain LMCOs are potentially involved in bacterial extracellular phenol oxidase activities and lignocellulose breakdown during agricultural waste composting.

Global Landscape of Total Organic Carbon, Nitrogen and Phosphorus in Lake Water

Human activities continue to increase the amount of carbon (C), nitrogen (N) and phosphorus (P) in lakes, which may cause serious environmental and human health problems. Global landscape of total organic C (TOC), N and P in lake water is still poorly known. Using a global data set that covers ~8300 lakes from 68 countries/regions spanning six continents, we estimate that global mean concentrations and storage in lake water are 5.578 mg L−1 and 984.0 Tg for TOC, 0.526 mg L−1 and 92.8 Tg for TN, and 0.014 mg L−1 and 2.5 Tg for TP. These lake elements are significantly interrelated and in uneven distribution, being associated with morphological characteristics and climate conditions. We proposed that global C, N and P cycles should be considered as a whole in biogeochemical studies and policy-making related to environmental protection.

Response of denitrifying genes coding for nitrite (nirK or nirS) and nitrous oxide (nosZ) reductases to different physico-chemical parameters during agricultural waste composting

The present research was performed to clarify the changes of denitrifying genes (nirK, nirS, and nosZ) abundances under different physico-chemical parameters through evaluating the relationships between the genes abundances and parameters during agricultural waste composting. The genes abundances were determined by real-time quantitative PCR (qPCR). The correlations between physico-chemical parameters and denitrifying genes abundances were analysed by regression analysis. qPCR results showed that the nosZ gene abundance was higher than that of nirK and nirS genes. The nirK gene abundance was higher than nirS gene indicating that nitrite reducers with Cu-containing enzyme encoded by nirK gene were more of importance than those with cytochrome cd1 nitrite reductase encoded by nirS gene in the nitrite reduction step. Regression analysis suggested that (1) nirK gene abundance was correlated with pile temperature following quadratic model; (2) nirS gene abundance was linearly correlated with pile temperature and concentration of NH4+, while correlated with concentration of NO3− and pH following inverse and quadratic model respectively; (3) nosZ gene abundance was quadratically correlated with pH and linearly correlated with water soluble carbon (WSC).

Hydrogen sulfide alleviates 2,4-dichlorophenol toxicity and promotes its degradation in Phanerochaete chrysosporium

In this study, the H2S donor, sodium hydrosulfide (NaHS) was used to pretreat Phanerochaete chrysosporium in order to improve its ability to degrade 2,4-dichlorophenol (2,4-DCP). When pretreated with 100μM NaHS, P. chrysosporium was able to degrade 2,4-DCP completely in 24h, whereas the degradation efficiency of the untreated control was only 57%. The 2,4-DCP-induced oxidative stress was alleviated by NaHS, and the percentage of surviving cells increased by 32%. H2S or HS(-), rather than other compounds derived from NaHS, were responsible for promoting 2,4-DCP degradation by P. chrysosporium. The results of this study suggest that H2S treatment is a potential strategy to alleviate environmental stress and improve the efficiency of the biological removal of pollutants from wastewater.

Study on binding modes between cellobiose and β-glucosidases from glycoside hydrolase family 1.

The hydrolysis of cellobiose by β-glucodisases is an important step of cellulose biodegradation. However, the interactive mechanism between cellobiose and β-glucosidases is still unclear until now. Thus, in this study, we explored the binding modes between cellobiose and three β-glucosidases from glycoside hydrolase family 1 by means of molecular docking. The three β-glucosidases were named as TmGH1 (from bacterium Thermotoga), SsGH1 (from archaea Sulfolobus solfataricus) and TrGH1 (from fungus Trichoderma reesei) respectively, according to the monophyletic groups they belong to. Molecular dockings were performed between cellobiose and the three β-glucosidases, resulting in three optimum docking complexes, that is TmGH1-cellobiose, SsGH1-cellobiose and TrGh1-cellobiose complexes. Our docking results indicated that there were non-bonded interactions between cellobiose and the three β-glucosidases. The binding affinities of the three complexes were -13.6669kJ/mol, -13.2973kJ/mol and -18.6492kJ/mol, respectively. Then the detailed interactions were investigated, which revealed the key amino acid residues interacted with cellobiose by hydrogen bonds (H-bonds) or hydrophobic interactions. It was observed that most of the key residues involved in the non-bonded interactions were equivalent and conserved for the three complexes, and these residues were a glutamine, a histidine, a tyrosine, a phenylalanine, three glutamics, and four tryptophans. This information is of great importance for designing β-glucosidase with higher cellobiose-hydrolyzing efficiency.