Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine

Background Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration. Methods A method of the substitution of “space” for “time” was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used. Results Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest in ER plots. Additionally, the Azorhizobium genus was only detected in the ER phase. Overall, our findings suggested that several rhizosphere microbial communities had significant differences among three natural restoration stages (ER, MR, and LR) and the rhizosphere bacterial communities mainly appeared in the early restoration stage can be preferred for remediation of pollution soil in Xikuangshan.

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Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

PLoS ONE ◽

10.1371/journal.pone.0257432 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257432

Author(s):

Li Jin ◽

Jian Lyu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Total N ◽

Rhizosphere Bacterial Community ◽

Healthy Growth ◽

Dominant Bacteria

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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Shift of millet rhizosphere bacterial community during the maturation of parent soil revealed by 16S rDNA high-throughput sequencing

Applied Soil Ecology ◽

10.1016/j.apsoil.2018.12.004 ◽

2019 ◽

Vol 135 ◽

pp. 157-165 ◽

Cited By ~ 8

Author(s):

Lixia Xu ◽

Yansha Han ◽

Min Yi ◽

Huilan Yi ◽

Erhu Guo ◽

...

Keyword(s):

Bacterial Community ◽

16S Rdna ◽

High Throughput ◽

High Throughput Sequencing ◽

Rhizosphere Bacterial Community

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Evaluation of bacterial diversity during fermentation process: a comparison between handmade and machine-made high-temperature Daqu of Maotai-flavor liquor

Annals of Microbiology ◽

10.1186/s13213-020-01598-1 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Qiancheng Zuo ◽

Yongguang Huang ◽

MinGuo

Keyword(s):

High Temperature ◽

Bacterial Diversity ◽

Relative Abundance ◽

Fermentation Process ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Functional Bacteria ◽

Significant Difference ◽

Fermentation Technology ◽

Molding Methods

Abstract Purpose High-temperature Daqu is a traditional fermentation starter that is used for Chinese Maotai-flavor Baijiu production. Although the bacteria in high-temperature Daqu are known to be responsible for developing the quality and flavor of Baijiu during the fermentation process, there is little information on the properties of the bacteria during the fermentation of high-temperature Daqu, especially machine-made high-temperature Daqu. This has limited the development of the Maotai-flavor Baijiu industry, particularly with regard to the mechanized production of Maotai-flavor Baijiu. Methods Illumina MiSeq high-throughput sequencing was applied to study bacterial compositions during the fermentation of handmade and machine-made high temperatures. Results The results show that bacterial diversity in machine-made Daqu was similar but higher than that in handmade Daqu at the end of fermentation, and there was no significant difference between the methods with regard to the dominant genera and their dynamic changes during fermentation. Rhizobium, Bacillus, Thermoactinomyces, Weissella, Lactobacillus, and Saccharopolyspora were the dominant genera during the fermentation of both Daqus, although the relative abundance of these dominant genera differed between the two methods. Interestingly, the machine-made Daqu contained a higher relative abundance of Bacillus than handmade Daqu at all fermentation times. Bacillus is the most important functional bacteria in the fermentation of Maotai-flavor Baijiu, suggesting that mechanical-molding methods could be applied to industrial Maotai-flavor Daqu production. Conclusion These results suggest that mechanical-molding methods could be applied to industrial Maotai-flavor Daqu production, which could be helpful for industrial Maotai-flavor Baijiu production and the development of fermentation technology.

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Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

mSystems ◽

10.1128/msystems.00721-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Tengxiang Lian ◽

Yingyong Huang ◽

Xianan Xie ◽

Xing Huo ◽

Muhammad Qasim Shahid ◽

...

Keyword(s):

Salt Stress ◽

Bacterial Community ◽

Management Practices ◽

High Throughput Sequencing ◽

Crop Productivity ◽

Soil Salinization ◽

Rrna Gene ◽

Content Type ◽

Rice Mutant ◽

Rhizosphere Bacterial Community

ABSTRACT Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

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Fecal bacterial community of finishing beef steers fed ruminally protected and non-protected active dried yeast

Journal of Animal Science ◽

10.1093/jas/skaa058 ◽

2020 ◽

Vol 98 (4) ◽

Author(s):

Tao Ran ◽

Peixin Jiao ◽

Ousama AlZahal ◽

Xiaolai Xie ◽

Karen A Beauchemin ◽

...

Keyword(s):

Bacterial Community ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Starch Content ◽

Feedlot Cattle ◽

Fecal Bacteria ◽

Beef Steers ◽

Fecal Samples ◽

Sequencing Platform ◽

Fecal Bacterial Community

Abstract Our previous study suggested that supplementation of high-grain diets with ruminally protected and non-protected active dried yeast (ADY) may potentially reduce manure pathogen excretion by feedlot cattle. We hypothesized that feeding ruminally protected ADY might change the fecal bacterial community of finishing cattle. The objective of this study was to investigate the effects of feeding ruminally protected and non-protected ADY to finishing beef steers on their fecal bacterial community. Fresh fecal samples were collected on day 56 from 50 steers fed one of five treatments: 1) control (no monensin, tylosin, or ADY), 2) antibiotics (ANT, 330 mg monensin + 110 mg tylosin·steer−1d−1), 3) ADY (1.5 g·steer−1d−1), 4) encapsulated ADY (EDY; 3 g·steer−1d−1), and 5) a mixture of ADY and EDY (MDY; 1.5 g ADY + 3 g EDY·steer−1d−1). Bacterial DNA was extracted from fecal samples and sequenced using a MiSeq high-throughput sequencing platform. A total number of 2,128,772 high-quality V4 16S rRNA sequences from 50 fecal samples were analyzed, and 1,424 operational taxonomic units (OTU) were detected based on 97% nucleotide sequence identity among reads, with 769 OTU shared across the five treatments. Alpha diversity indices, including species observed, Chao estimate, abundance-based coverage estimator, Shannon, Simpson, and coverage, did not differ among treatments, and principal coordinate analysis revealed a high similarity among treatments without independent distribution. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) for greater relative abundance of Bacteroidetes but lesser Firmicutes with ANT, EDY, and MDY compared with control steers. Prevotella was the dominant genus in all treatments and steers supplemented with ANT, EDY, and MDY had greater (P < 0.05) relative abundance of Prevotella than control steers, but lesser (P < 0.03) relative abundance of Oscillospira. No differences between ADY and control were observed for the aforementioned variables. Fecal starch contents were not different among treatments, but the relative abundance of Bacteroidetes, as well as Prevotella at genera level, tended (P < 0.06) to be positively correlated to fecal starch content. We conclude that supplementing ruminally protected or non-protected ADY or ANT had no effect on diversity and richness of fecal bacteria of finishing beef cattle, whereas feeding protected ADY or ANT to finishing beef steers altered the dominant fecal bacteria at phylum and genus levels. Therefore, supplementation of ruminally protected ADY may potentially improve intestinal health by stimulating the relative abundance of Prevotella.

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Effects of a Superabsorbent Resin with Boron on Bacterial Diversity of Peat Substrate and Maize Straw

BioMed Research International ◽

10.1155/2018/6071085 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Yuxin Wang ◽

Chaonan Wang ◽

Yanan Zhao ◽

Pingzhi Wang

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

High Throughput Sequencing ◽

Community Diversity ◽

Original Structure ◽

Strengthening Effect ◽

Theoretical Support ◽

Maize Straw ◽

New Type ◽

Superabsorbent Resin

As a chemical water-saving material, superabsorbent resin is often applied to improve soil physicochemical properties for the purpose of promoting crop growth. In this study, a new type of superabsorbent resin with boron (SARB) was used as a functional material mixed with peat substrate and maize straw in percentages (mass ratio) of 0.05%, 0.1%, 0.15%, and 0.2%, respectively, and high-throughput sequencing technology was used to test bacterial diversity, analyzing and exploring ecological safety of the superabsorbent resin with boron (SARB) in order to provide theoretical support for field applications. The research results show that the superabsorbent resin with boron (SARB) can promote bacterial community diversity in the maize straw. In ten treatments, Proteobacteria accounted for the absolute advantage of the bacterial population in the CT group and in the JG group. However, the superabsorbent resin with boron (SARB) synthesized in the laboratory cannot change the original structure of the bacterial community and has scarcely any toxic effect on the bacterial community in both peat substrate and maize straw, and, indeed, it has a strengthening effect on Proteobacteria and Actinobacteria and a weakening effect on Acidobacteria and Firmicutes to some extent.

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Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

AMB Express ◽

10.1186/s13568-021-01323-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xu Jiang ◽

Hui Ma ◽

Qing-lei Zhao ◽

Jun Yang ◽

Cai-yun Xin ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Relative Abundance ◽

Paddy Soil ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Available Phosphorus ◽

Uncultured Bacterium ◽

Ditch Sediment

AbstractAs an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.

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Regulating Soil Bacterial Diversity, Enzyme Activities and Community Composition Using Residues from Golden Apple Snails

10.1101/692822 ◽

2019 ◽

Author(s):

Jiaxin Wang ◽

Xuening Lu ◽

Jiaen Zhang ◽

Guangchang Wei ◽

Yue Xiong

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Soil Nutrients ◽

Soil Ph ◽

Relative Abundance ◽

Enzyme Activities ◽

Bacterial Community Composition ◽

Apple Snail ◽

Low Levels

AbstractGolden apple snails (GAS) have become a serious pest for agricultural production in Asia. A sustainable method for managing GAS is urgently needed, including potentially using them to produce commercial products. In this study, we evaluate the effects of GAS residues (shell and meat) on soil pH, bacterial diversity, enzyme activities, and other soil characteristics. Results showed that the amendment of GAS residues significantly elevated soil pH (to near-neutral), total organic carbon (TOC) (by 10-134%), NO3-N (by 46-912%), NH4-N (by 18-168%) and total nitrogen (TN) (by 12-132%). Bacterial diversity increased 13% at low levels of amendment and decreased 5% at high levels, because low-levels of GAS residues increased soil pH to near-neutral, while high-levels of amendment substantially increased soil nutrients and subsequently suppressed bacterial diversity. The dominant phyla of bacteria were: Proteobacteria (about 22%), Firmicutes (15-35%), Chloroflexi (12%-22%), Actinobacteria (8%-20%) Acidobacteria, Gemmatimonadetes, Cyanobacteria and Bacterioidetes. The amendment of GAS residues significantly increased the relative abundance of Firmicutes, Gemmatimonadetes, Bacterioidetes and Deinococcus-Thermus, but significantly decreased the relative abundance of Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria and Planctomycetes. Our results suggest that GAS residues treatment induces a near-neutral and nutrient-rich soil. In this soil, soil pH may not be the best predictor of bacterial community composition or diversity; rather soil nutrients (ie., NH4-N and NO3-N) and soil TOC showed stronger correlations with bacterial community composition. Overall, GAS residues could replace lime for remediation of acidic and degraded soils, not only to remediate physical soil properties, but also microbial communities.ImportanceThe wide spreading golden apple snail (GAS) is a harmful pest to crop productions and could result in soil and air pollutions after death. In the previous study, we developed a biocontrol method: adding GAS residues to acidic soil to mitigate the living GAS invasion and spread, improve soil quality, and reduce soil and air pollution. However, the effects of GAS residues amendment on bacterial diversity and community still remain unclear. This study provided insights into bacterial diversity and community compositions to facilitate the evaluation of GAS residues application.

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Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽

10.7717/peerj.4514 ◽

2018 ◽

Vol 6 ◽

pp. e4514 ◽

Cited By ~ 25

Author(s):

Jun Lou ◽

Li Yang ◽

Haizhen Wang ◽

Laosheng Wu ◽

Jianming Xu

Keyword(s):

Bacterial Community ◽

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Laboratory Strain ◽

Soil Bacterial Community ◽

Absolute Abundance ◽

Internal Reference ◽

Biodegradation Study ◽

Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

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Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing

PeerJ ◽

10.7717/peerj.9122 ◽

2020 ◽

Vol 8 ◽

pp. e9122

Author(s):

Li Chen ◽

Yuzhu Li ◽

Lei Jin ◽

Li He ◽

Xiaolin Ao ◽

...

Keyword(s):

Bacterial Community ◽

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Middle Layer ◽

Ammonia Nitrogen ◽

Western China ◽

Rrna Gene ◽

Linear Discriminant ◽

Pit Mud

“Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.

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