Aims: The former Mamut Copper Mine, acid mine drainage site represents an anthropogenic altered landscape characterized by its acidic topsoil which is contaminated primarily with copper. Even though the mining operation was ceased at 1999, the bacterial diversity in this area has never been investigated. This study was conducted to ascertain the bacterial diversity of this abandoned copper mine and correlate it to the copper concentration in the soil. Methodology and results: Soil samples were collected from 7 sites near the mine pit and the vicinity. Soil samples were assessed for soil copper elemental concentration using inductively coupled plasma optical emission spectrometry and bacteria were isolated via serial dilution followed by culture on nutrient agar plates. Phylogenetic analysis was done based on the full-length sequences of 16S rRNA gene. Twenty-four phylotypes were obtained from the 7 locations which originated from the phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The results of the study indicated that site 2 (6.030223°; 116.658030°), located in between the mine pit and the mine factory with a copper concentration of 88.96 ppm, possessed the most diverse bacterial community with a Shannon diversity index (H) of 1.68, evenness (EH) of 0.94 and richness (S) of 6. Conclusion, significance and impact of study Current study revealed that there was a positive correlation between the copper concentration and the H index and the richness, but this was not reflected in the evenness. This is the first report of bacterial diversity from the former Mamut Copper Mine site. The data provided a valuable insight for the future monitoring of the bacterial community in this ecologically important niche.
Soil Microbiology

Aims: Intercropping system in oil palm plantation is recognized as one of a nature-based solution as well as a promising sustainable practice. This study aimed to observe the advantages of existing intercropping system in one of North Sumatra’s oil palm plantation. It is achieved by analyzing the population of soil bacteria and fungi in oil palm intercropping fields with sorghum and cassava, compared with the non-intercropping field that using Mucuna bracteata (MB) as a common legume cover crop in oil palm plantations. Methodology and results: Soil samples were collected from the weeded circle and windrow area (the area between palms within the row). The results showed that the highest and the lowest soil bacteria populations were in sorghum (1.7 ± 1.4 × 108 CFU/g) and MB (1.7 ± 0.4 × 107 CFU/g), while the highest and the lowest soil fungi populations were in sorghum (4.3 ± 2.9 × 106 CFU/g) and cassava (2.1 ± 0.8 × 106 CFU/g). Conclusion, significance and impact of study The intercropping system in this study showed a significant difference in the bacteria population, while the fungi population had no difference compared to the non-intercropping system. The bacterial and fungi population results also indicate that the intercropping system potentially enhances the soil's biological activity as an indicator of improved soil health. It is also followed by a slightly higher soil organic carbon value in intercropping system. This research suggests that further studies should be done to identify specific soil functional microbes (nutrients fixers and solubilizers). The future research will be used as a reference for promising biofertilizer agents in supporting sustainable crop production.
Palm Oil ; Soil Microbiology

Aims: Meloidogyne incognita adversely affects numerous crop plants worldwide. Therefore, the modern world has been moving towards biocontrol methods to prevent nematode attacks. This study was aimed to (i) investigate the potential use of Trichoderma harzianum NFCF160 and T. virens Isf-77 in managing M. incognita in soil and (ii) identify trapping mechanisms employed by both Trichoderma strains to suppress M. incognita. Methodology and results: Three weeks old, Basella alba L. plants were subjected to five different treatments. The above and below ground growth parameters and the galling indices of these plants were measured every four weeks for three sampling times. Trapping mechanisms employed by Trichoderma strains were examined following plate assays. Plants treated with T. harzianum NFCF160 and T. virens Isf-77 had significantly higher values for the total number of leaves (34 ± 2.84) and (27 ± 2.61), fresh weight of the shoot (81 ± 9.51 g) and (91 ± 9.70 g), dry weight of the shoot (71 ± 5.24 g) and (62 ± 5.81 g), respectively eight weeks after inoculation of M. incognita. Significantly low galling indices (2 and 2) were recorded in B. alba treated with Trichoderma strains. Both Trichoderma strains exhibited various nematode-trapping mechanisms, such as non-constricting rings and adhesive spores. Conclusion, significance and impact of study This investigation highlighted the potential of both Trichoderma strains as biocontrol agents to control M. incognita effect in sustainable agriculture.
Tylenchoidea ; Trichoderma ; Soil Microbiology

Soil microorganisms are one of the important biological indictors of soil quality and can reflct the comprehensive ecological environment characteristics of the soil. The research of soil microbial diversity is the key to know the ecological functions and balance with soil. In this paper, high-throughput sequencing on PCR-amplified 16 S rRNA gene V3-V4 fragments was used to determine the bacterial diversity in rhizosphere soil of A. macrocephala under the treatment with BZJN1 or streptoprofen. The results showed that there were no significant differences of the bacteria in A. macrocephala rhizosphere soil of the streptoprofen treatment group and the biocontrol BZJN1 treatment group. All the soil bacteria was classified into 25 categories,67 classes, 108 orders, 167 families and 271 generas, except some unidentified bacteria. Proteobacteria(30.7%-34.8%) was the dominant phylum, of which Alphaproteobacteria(16.8%-18.5%) was the dominant subgroup. Compared with the control group, the relative abundance of multiple phylums bacteria in the rhizosphere soil of A. macrocephala was significantly changed in the streptoprofen treatment group and the biocontrol BZJN1 treatment group. In addition, RDA analysis showed that there was connection with different environmental factors and microbial communities. The abundance of the three genera in the rhizosphere soil of A. macrocephala was significantly positively correlated with Invertase, Urease and AP. PICRUSt function prediction results showed that BZNJ1 could enhance some bacterial functions and promote the plant growth. Biocontrol is a new type of green and safety control pest method. BZNJ1 significantly enhances some bacterial functions on the basis of effectively preventing root rot of A. macrocephala and promoting plant growth, and has no significant effect on the soil bacterial community structure. All the results can provide theoretical support for popularization of BZNJ1.
Atractylodes ; Bacteria ; Rhizosphere ; Soil ; Soil Microbiology

Bioremediation is considered as a cost-effective, efficient and free-of-secondary-pollution technology for petroleum pollution remediation. Due to the limitation of soil environmental conditions and the nature of petroleum pollutants, the insufficient number and the low growth rate of indigenous petroleum-degrading microorganisms in soil lead to long remediation cycle and poor remediation efficiency. Bioaugmentation can effectively improve the biodegradation efficiency. By supplying functional microbes or microbial consortia, immobilized microbes, surfactants and growth substrates, the remediation effect of indigenous microorganisms on petroleum pollutants in soil can be boosted. This article summarizes the reported petroleum-degrading microbes and the main factors influencing microbial remediation of petroleum contaminated soil. Moreover, this article discusses a variety of effective strategies to enhance the bioremediation efficiency, as well as future directions of bioaugmentation strategies.
Biodegradation, Environmental ; Petroleum ; Soil ; Soil Microbiology ; Soil Pollutants

With continuous improvement of people's living standards, great efforts have been paid to environmental protection. Among those environmental issues, soil contamination by petroleum hydrocarbons has received widespread concerns due to the persistence and the degradation difficulty of the pollutants. Among the various remediation technologies, in-situ microbial remediation enhancement technologies have become the current hotspot because of its low cost, environmental friendliness, and in-situ availability. This review summarizes several in-situ microbial remediation technologies such as bioaugmentation, biostimulation, and integrated remediation, as well as their engineering applications, providing references for the selection of in-situ bioremediation technologies in engineering applications. Moreover, this review discusses future research directions in this area.
Biodegradation, Environmental ; Humans ; Hydrocarbons ; Petroleum ; Soil ; Soil Microbiology ; Soil Pollutants

The continuous cropping obstacle of Gastrodia elata is outstanding, but its mechanism is still unclear. In this study, microbial changes in soils after G. elata planting were investigated to explore the mechanism correlated with continuous cropping obstacle. The changes of species and abundance of fungi and bacteria in soils planted with G. elata after 1, 2, and 3 years were compared. The pathogenic fungi that might cause continuous cropping diseases of G. elata were isolated. Finally, the prevention and control measures of soil-borne fungal diseases of G. elata were investigated with the rotation planting pattern of "G. elata-Phallus impudicus". The results showed that G. elata planting resulted in the decrease in bacterial and fungal community stability and the increase in harmful fungus species and abundance in soils. This change was most obvious in the second year after G. elata planting, and the soil microbial community structure could not return to the normal level even if it was left idle for another two years. After G. elata planting in soils, the most significant change was observed in Ilyonectria cyclaminicola. The richness of the Ilyonectria fungus in soils was significantly positively correlated with the incidence of G. elata diseases. When I. cyclaminicola was inoculated in the sterile soil, the rot rate of G. elata was also significantly increased. After planting one crop of G. elata and one to three crops of P. impudicus, the fungus community structure in soils gradually recovered, and the abundance of I. cyclaminicola decreased year by year. Furthermore, the disease rate of G. elata decreased. The results showed that the cultivation of G. elata made the Ilyonectria fungi the dominant flora in soils, and I. cyclaminicola served as the main pathogen of continuous cropping diseases of G. elata, which could be reduced by rotation planting with P. impudicus.
Bacteria ; Fungi ; Gastrodia/microbiology* ; Mycobiome ; Soil ; Soil Microbiology

The development of bioremediation for contaminated soil in China during past 30 years was briefly reviewed, mainly including the developing stages, bioremediation techniques/strategies and their applications, and isolation, screening and characterizations of microbial strains for bioremediation as well as their efficiencies in bioremediation of contaminated soils. Finally, future development of bioremediation techniques/strategies and their applications were also discussed.
Biodegradation, Environmental ; China ; Environmental Pollution ; Soil Microbiology ; Soil Pollutants

The natural forest and artificial shed are the main cropping modes of Coptis chinensis. This study is aimed to reveal the rhizosphere soil bacterial community structure difference between under tow C. chinensis cropping modes-natural forest and artificial shed, and to assist us to completely understand soil quality condition,and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under tow cropping modes-natural forest and artificial shed were collected. Illumina high-throughput sequencing technology was used to analyze the alpha diversity, community composition, community structure of soil bacteria under the tow cropping modes,and the effects of soil nutriment indices on soil bacterial community structure. Through the analysis of species number, Shannon, Chao1 index and ACE index of bacterial community, it was found that the bacterial diversity of 1-year-old C. chinensis soil under natural forest cropping mode was significantly lower than that under artificial shed cropping mode, and the diversity of bacterial communities in soil of 2-5-years old C. chinensis were not significant different between two cropping modes. A total of 53 phyla,60 classes,140 orders and 266 families were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest, respectively. The rhizosphere soil of C. chinensis under the cropping modes of artificial shed included 54 phyla,65 classes,140 orders and 264 families, respectively. Under the two cropping modes, the top 10 dominant species of bacterial community abundance are the same, they are Proteobacteria, Acidobacteria, Actinobacteria,Bacteroidetes, Planctomycetes, Chloroflexi, Verrucomicrobia, Gemmatimonadetes, Firmicutes and Cyanobacteria, but there are differences in the abundance sequence. The top 10 dominant species of bacterial community abundance accounted for 74.36% to 74.30% of the total bacteria, and 3.15% to 3.92% of the bacteria are unclassified. The results of Metastat analysis showed that the abundance of Gemmatimonadetes in the rhizosphere soil of C. chinensis under the cropping modes the artificial shed was significantly higher than that under the natural forest cropping mode(P<0.05). MRPP analysis of community structure differences showed that under tow cropping modes, there were significant differences in the bacterial community structure of 1-4-year-old soil bacteria, among which the difference between 1-year-old soil samples was the largest. With the increase of cropping years, the difference gradually decreases, and there is no significant difference in the bacterial community structure between 5-year-old soil samples. RDA analysis and correlation analysis of bacterial community structure and soil physical and chemical properties showed that the order of environmental factors on the rhizosphere soil bacteria of Coptis chinensis was: pH>available P> total P> total K>bulk density>total N>available N>organic matter. The results are helpful to understand the soil health of C. chinensis and provide scientific basis and theoretical guidance for soil improvement and C. chinensis planting.
Child, Preschool ; Coptis ; Forests ; Humans ; Infant ; Rhizosphere ; Soil ; Soil Microbiology

Continuous planting of muskmelon and excessive application of chemical fertilizers have caused a series of problems, such as imbalance of the soil micro-ecological environment, serious soil-borne diseases and yield loss. Application of Bacillus subtilis agent is an important way to improve soil micro-ecological environment, prevent soil-borne diseases, and promote plant growth. In this study, B. subtilis was used as experimental agent to analyze the effects of different application methods on the soil microbial diversity and growth of muskmelon in greenhouse. The number of culturable microorganisms in soil was measured by dilution-plate method. The diversity of soil uncultivated microorganisms was determined by Illumina Miseq sequencing technology. The yield of muskmelon was measured by weighing method. The number of culturable bacteria in the root irrigation, hole application and dipping root application groups was higher than that of the control in different muskmelon growth stages, but there was no significant difference among the three different application methods. The number of soil fungi from B. subtilis agent treatment groups in flowering stage was significantly lower in comparison to the control group. However, B. subtilis agent treatment did not cause significant difference on soil fungi number at the fruiting and pulling stage. Diversity analysis of uncultured microorganisms showed that the Shannon index values of bacteria were higher and Simpson index values were lower respectively in the three B. subtilis treatment groups than that in the control. Moreover, the dipping root treatment produced the lowest Shannon index value and the highest Simpson index value of fungi. NMDS and cluster analysis showed that B. subtilis agents dipping root treatment significantly affected the bacterial and fungal flora, both of which were clustered into one independent branch. The application of B. subtilis agents, especially dipping root treatment, significantly decreased the abundance of Bacteroidetes, increased the abundance of Actinobacteria and Acidobacteria. The B. subtilis agent treatment didn't produce significant effect on the diversity of fungal flora except Chytridiomycota. The height, stem diameter and leaf area of muskmelon increased by applying B. subtilis agents, and dipping root treatment produced the most significant effect. As a new type of environmental protection fertilizer, B. subtilis agent can increase the number of soil culturable microorganisms, improve soil microbial diversity, and promote growth and yield. This study would provide a scientific basis for the rational application of B. subtilis.
Bacillus subtilis/genetics* ; Fertilizers ; Fungi ; Soil ; Soil Microbiology