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

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.

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

PLoS ONE ◽

10.1371/journal.pone.0259515 ◽

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.

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

Applied Sciences ◽

10.3390/app11030918 ◽

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.

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A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa200 ◽

2020 ◽

Vol 96 (11) ◽

Author(s):

Jianxiao Song ◽

Uli Klümper ◽

Leise Riber ◽

Arnaud Dechesne ◽

Barth F Smets ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Amplicon Sequencing ◽

Plasmid Transfer ◽

Rrna Gene ◽

Long Term Effects ◽

Cu Contamination ◽

Soil Bacterial

ABSTRACT Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg−1) soil compared to corresponding communities extracted from moderately (458 mg kg−1) Cu contaminated soil and a low Cu reference soil (15 mg kg−1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.

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

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18168661 ◽

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.

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