Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

Nacke, Heiko; Thürmer, Andrea; Wollherr, Antje; Will, Christiane; Hodač, Ladislav; Herold, Nadine; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

doi:10.1371/journal.pone.0017000

Cited by 487 publications

(393 citation statements)

References 51 publications

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“…In our work, we find that in high levels of Cd contamination soil, the species richness, diversity, and evenness of bacterial communities are lower compared to the unpolluted ones in the idle soil group, which matches those reported by Nacke et al (2011) andWill et al (2010). According to the rarefaction curves in Fig.…”

Section: Discussionsupporting

confidence: 87%

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium

et al. 2018

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Purpose This investigation aimed to estimate and characterize the microbial diversity in soils with cadmium (Cd) at different concentrations and to evaluate whether Brassica napus can restore the soil microbial diversity. Materials and methods We conducted the pot experiment to analyze the composition of microbial communities in the soil contaminated with 0, 1, and 2 mg/kg Cd, as well as planted with oilseed rape. The bacterial and fungal communities were characterized via next-generation sequencing based on 16S and 18S rRNA gene fragments pyrosequencing, respectively. Results and discussion The results show that cadmium contamination decreased both the microbial richness and diversity in the soil, while the cultivation of oilseed rape increased the richness and diversity. In bacteria, Proteobacteria was the most abundant phylum in all the samples accounting for 39.62 to 46.14%, followed by Bacteroidetes, Actinobacteria, and Chloroflexi. These phyla collectively comprised more than 70% of all phyla. Ascomycota was the most abundant phylum in all samples in fungi (89.65 to 96.00%), and it was the only phylum whose abundance was increased with the rise of Cd concentration. Conclusions Microbial richness and diversity were affected by the combined action of Cd and B. napus. Cd contamination decreased the microbial richness and diversity, while cropping with oilseed rape increased the microbial richness and diversity, which alleviated the deleterious effect of the Cd pollution in soils. These reflected that oilseed rape played a positive role in maintaining species diversity of microorganism from the side.

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Section: Discussionsupporting

confidence: 87%

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium

et al. 2018

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“…The top two abundant phyla of bacteria were Acidobacteria and Proteobacteria through all the samples (Figure 2), and the abundance ranks of the two phyla agreed with those of 88 soil samples in North and South America (Lauber et al, 2009) as well as with those of forest and grassland soil samples in Germany (Nacke et al, 2011). The top two abundant phyla were Actinobacteria and Bacteriodetes identified in the soil samples of Texas (USA) where different agronomic and chemical management had been implemented (Girvan et al, 2003).…”

Section: Discussionmentioning

confidence: 52%

“…Bacterial diversity is very high in soils (Gans et al, 2005), where up to 6,000-50,000 bacterial species were estimated to be present in one gram of soil samples (Claire et al, 2003). Bacteria play important roles in biogeochemical cycles, supplying nutrients to crops and keeping soil health in agricultural ecosystems (Kennedy et al, 1995;Nacke et al, 2011). Additionally, fungal pathogens can easily accumulate in continuous cropping systems (Chen et al, 2012;Zhou et al, 2012).…”

Section: Introduction Lmentioning

confidence: 99%

“…Previous studies have shown that soil microbial communities were affected by miscellaneous factors, including soil types (Girvan et al, 2003), plant spe-cies (Garbeva et al, 2006), temperature (Norris et al, 2002), organ amendments (Stark et al, 2007), nitrogen levels (Fierer et al, 2012), soil pH (Lauber et al, 2009;Nacke et al, 2011) and contaminations (Lee et al, 2011). Recently, an increasing number of studies have revealed that continuous cropping cause destruction of soil microbial community size and structure (Lu et al, 2013;.…”

Section: Introduction Lmentioning

confidence: 99%

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Application of Deep Pyrosequencing to the Analysis of Soil Microbial Communities in Different Lotus Fields

Cui¹,

Wang²,

Zeng³

et al. 2016

JRST

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Fusarium oxyporum f. sp. nelumbicola is a very important plant pathogen that can cause lotus Fusarium wilt and lead to vast economic loss in Jiangxi Province, china. Sequencing data of 16S ribosomal Rna genes and internal transcribed spacer regions revealed that different bacterial and fungal communities were present in soil samples from healthy or Fusarium wilt-infected lotus fields with different years of continuous cropping, indicating that the long-term continuous cropping of lotus significantly altered the soil microbial communities. Fungal diversity indexes in the healthy soil samples increased with the years of monoculture, but decreased in the Fusarium wilt-infected soil samples, whereas bacterial community diversity in all the soil samples was relatively stable. a cluster analysis revealed that consecutive cropping time was a key factor for determining fungal community structure, but not for bacterial community structure. The relative abundances of Proteobacteria, Acidobacterial, Ascomycota, and Basidiomycota phyla decreased with the years of lotus monoculture. compared with the healthy soil samples, the abundances of beneficial bacteria in the Fusarium wilt-infected soil samples significantly decreased with time. These observations indicate that soil weakness and lotus Fusarium wilt disease may be attributed to structural changes of soil microbial communities after long-term continuous cropping, and the changes include reduction of beneficial microorganisms and accumulation of fungal pathogens.

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“…Fortunately, Illumina high-throughput sequencing has enabled the in-depth exploration of microbial biodiversity in the environment (Nacke et al 2011;Chen et al 2014a). This technology is capable of significantly expanding the detection range of low-abundance taxas in the community, which are generally not available by conventional molecular methods.…”

Section: Introductionmentioning

confidence: 99%

Shifts in indigenous microbial communities during the anaerobic degradation of pentachlorophenol in upland and paddy soils from southern China

Chen

Tao

et al. 2016

Environ Sci Pollut Res

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Pentachlorophenol (PCP) is a common persistent pesticide in soil that has generated a significant environmental problem worldwide. Therefore, anaerobic degradation of PCP by the soil indigenous microbial community has gained increasing attention. However, little information is available concerning the functional microorganisms and the potential shifts in the microbial community associated with PCP degradation. In this study, we conducted a set of experiments to determine which components of the indigenous microbial community were capable of degrading PCP in soils of two land use types (upland and paddy soils) in southern China. Our results showed that the PCP degradation rate was significantly higher in paddy soils than that in upland soils. 16S ribosomal RNA (rRNA) high-throughput sequencing revealed significant differences in microbial taxonomic composition between the soil with PCP and blank (soil without PCP) with Acinetobacter, Clostridium, Coprococcus, Oxobacter, and Sedimentibacter dominating the PCP-affected communities. Acinetobacter was also apparently enriched in the paddy soils with PCP (up to 52.2 %) indicated this genus is likely to play an important role in PCP degradation. Additionally, the Fe(III)-reducing bacteria Clostridium may also be involved in PCP degradation. Our data further revealed hitherto unknown metabolisms of potential PCP degradation by microorganisms including Coprococcus, Oxobacter, and Ruminiclostridium. Overall, these findings indicated that land use types may affect the PCP anaerobic degradation rate via the activities of indigenous bacterial populations and extend our knowledge of the bacterial populations responsible for PCP degradation.

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Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

Cited by 487 publications

References 51 publications

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium

Application of Deep Pyrosequencing to the Analysis of Soil Microbial Communities in Different Lotus Fields

Shifts in indigenous microbial communities during the anaerobic degradation of pentachlorophenol in upland and paddy soils from southern China

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