scholarly journals Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland

2021 ◽  
Vol 18 (16) ◽  
pp. 8661
Author(s):  
Shu-chun Tseng ◽  
Chih-ming Liang ◽  
Taipau Chia ◽  
Shan-shin Ton
Keyword(s):  
Heavy Metal ◽  
Bacterial Community ◽  
Structural Changes ◽  
Ph Value ◽  
Deep Layer ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Zinc Tolerance ◽  
Copper And Zinc ◽  
Soil Bacterial

The structural changes of microorganisms in soil are the focus of soil indicators research. The purpose of this study was to investigate the changes in the composition of the soil bacterial community in heavy metal-contaminated soil. A total of six soil samples (two sampling times) were collected from contaminated farmland at three different depths (surface, middle, and deep layer). The pH value was measured. The concentrations of heavy metals (Cr, Ni, Cu, Zn, Cd, and Pb) and the soil bacterial community were analyzed using ICP-OES and 16S rRNA gene sequencing. The results of the two samplings showed that the pH value in the deep layer decreased from 6.88 to 6.23, and the concentrations of Cu, Zn, Cd, and Pb, with a smaller ion radius, increased by 16–28%, and Shannon, Chao1 increased by ~13%. The bacteria community composition at the three depths changed, but Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla. In the copper and zinc tolerance test, the isolated bacterium that was able to tolerate copper and zinc was Bacillus sp. We found that, the longer the heavy metal pollution was of concern, the higher the tolerance. These results can be used as references for the microbial remediation of heavy metal-contaminated farmland.

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

Drivers on The Halophytes' Rhizosphere Bacteria Community and Functions in North China Salinized Areas

2021 ◽  
Author(s):  
Fating Yin ◽  
Fenghua Zhang ◽  
Zhibo Cheng ◽  
Haoran Wang
Keyword(s):  
Bacterial Community ◽  
North China ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Rhizosphere Soil ◽  
Ph Value ◽  
Northern China ◽  
Soil Bacterial Community ◽  
Leymus Chinensis ◽  
Soil Bacterial

Abstract Soil salinity is a serious environmental issue in arid China. Soil bacteria play a fundamental role in soil systems and respond rapidly to environmental changes. However, the responses of soil bacterial community to the different halophytes remains poorly understood. We investigated rhizosphere soil bacterial community changes under different halophytes in north China using high-throughput sequencing. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, and Chloroflexi across three halophytic vegetation. These bacteria have important assistance for halophytes adapt to saline soil. PICRUSt forecasts demonstrated that energy metabolism, amino acid metabolism and carbohydrate metabolism are main bacterial functions in halophyte vegetation soil, and the abundance of metabolism these bacterial functions in SG was significantly higher than that in LC and PT. The pH value of different halophyte rhizosphere soils has a more significant effect on bacterial diversity than EC and soil trophic status, and soil water content (SWC) was important effect factors leading to differences in bacterial functions. These results give us a deeper understanding of the diversity and functional differences of rhizosphere soil bacterial communities in the typical halophytic vegetation of northern China.

scholarly journals Niche Selection by Soil Bacterial Community of Disturbed Subalpine Forests in Western Sichuan

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 505
Author(s):  
Zheliang Sheng ◽  
Wanze Zhu ◽  
Huaiying Yao ◽  
Shumiao Shu ◽  
Xia Li ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Secondary Forest ◽  
Soil Bacterial Community ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Western Sichuan ◽  
Local Soil ◽  
Soil Bacterial

Soil bacterial microbial communities are important in the ecosystem function and succession of forests. Using high-throughput 16S rRNA gene sequencing and relative importance for linear regression, we explored how the structures of soil bacterial community were influenced by the environmental factors and restoration succession of secondary forests in the Miyaluo Mountains of western Sichuan, China. Using a space-for-time approach, field measurements and sampling were conducted in four stands at different stages of natural restoration. Results of distance-based multivariate analysis showed that soil pH, organic carbon, available phosphorus, and C/N ratio were the predominant environmental factors that collectively explained a 46.9% variation in the bacterial community structures. The community compositions were jointly controlled by the direct and indirect effects of the rehabilitation stages. The changes in soil environmental factors coincided with restoration succession could lead to the shifts in the relative abundance of different soil bacterial taxa. We screened 13 successional discriminant taxa that could quantitatively indicate the secondary succession subalpine stage. Collectively, our findings show that soil bacteria in different taxa are governed by different local soil variables and rehabilitation ages, which can lead to shifts in the relative abundance of different taxa in successional stages, ultimately changing the entire soil bacterial community with the succession of secondary forest.

Heavy Metal Pollution Structures Soil Bacterial Community Dynamics in SW Spain Polluted Salt Marshes

2016 ◽  
Vol 227 (12) ◽  
Author(s):  
Jennifer Mesa ◽  
Enrique Mateos-Naranjo ◽  
Eloísa Pajuelo ◽  
Miguel Ángel Caviedes ◽  
Ignacio David Rodríguez-Llorente
Keyword(s):  
Heavy Metal ◽  
Bacterial Community ◽  
Salt Marshes ◽  
Metal Pollution ◽  
Heavy Metal Pollution ◽  
Community Dynamics ◽  
Soil Bacterial Community ◽  
Sw Spain ◽  
Bacterial Community Dynamics ◽  
Soil Bacterial

scholarly journals Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259515
Author(s):  
Fating Yin ◽  
Fenghua Zhang ◽  
Haoran Wang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Acid Metabolism ◽  
Rhizosphere Soil ◽  
Soil Bacterial Community ◽  
Rhizosphere Bacteria ◽  
Community Diversity ◽  
Rrna Gene ◽  
Soil Bacterial ◽  
Suaeda Glauca

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

scholarly journals Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters

2008 ◽  
Vol 75 (3) ◽  
pp. 668-675 ◽  
Author(s):  
Sergio E. Morales ◽  
Theodore F. Cosart ◽  
Jesse V. Johnson ◽  
William E. Holben
Keyword(s):  
Bacterial Community ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Soil Bacterial Community ◽  
Community Diversity ◽  
Sequence Length ◽  
Rrna Gene ◽  
Ecological Parameters ◽  
Soil Bacterial ◽  
Analytical Approaches

ABSTRACT To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.

scholarly journals Impact of Rocky Desertification Control on Soil Bacterial Community in Karst Graben Basin, Southwestern China

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiang Li ◽  
Ang Song ◽  
Hui Yang ◽  
Werner E. G. Müller
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Control Area ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Natural Ecosystem ◽  
Rocky Desertification ◽  
Soil Bacterial Communities ◽  
Edaphic Properties ◽  
Soil Bacterial

Microorganisms play critical roles in belowground ecosystems, and karst rocky desertification (KRD) control affects edaphic properties and vegetation coverage. However, the relationship between KRD control and soil bacterial communities remains unclear. 16S rRNA gene next-generation sequencing was used to investigate soil bacterial community structure, composition, diversity, and co-occurrence network from five ecological types in KRD control area. Moreover, soil physical-chemical properties and soil stoichiometry characteristics of carbon, nitrogen and phosphorus were analyzed. Soil N and P co-limitation decreased in the contribution of the promotion of KRD control on edaphic properties. Though soil bacterial communities appeared strongly associated with soil pH, soil calcium, soil phosphorus and plant richness, the key factor to determine their compositions was the latter via changed edaphic properties. The co-occurrence network analysis indicated that soil bacterial network complexity in natural ecosystem was higher than that in additional management ecosystem. Candidatus Udaeobacter, Chthoniobacterales, and Pedosphaeraceae were recognized as the key taxa maintaining karst soil ecosystems in KRD control area. Our results indicate that natural recovery is the suitable way for restoration and rehabilitation of degraded ecosystems, and thus contribute to the ongoing endeavor to appraise the interactions among soil-plant ecological networks.

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