Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

Sun, Xiaoxu; Song, Benru; Xu, Rui; Zhang, Miaomiao; Gao, Pin; Lin, Hanzhi; Sun, Weimin

doi:10.1016/j.jes.2020.12.019

Cited by 61 publications

(31 citation statements)

References 68 publications

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“…On balance, our results showed that the effect of the pollutants on the endophytic bacterial communities was minimal ( Figure 5 ). Similar results were also found in a previous study on other species, such as Miscanthus sinensis ( Sun et al, 2021 ). This indicates that the composition of endophytic microorganisms seemed to be more easily influenced by the plants themselves than by external environmental conditions, highlighting the importance of the plant selection effect on its colonized endophytes ( Turner et al, 2013 ).…”

Section: Resultssupporting

confidence: 91%

“…In the original soil, the Chao1 index was 3089.47 with the microbial communities were mainly composed of Firmicutes (30.4%), Proteobacteria (29.7%), Actinobacteria (11.0%), Acidobacteria (8.2%), Bacteroidetes (4.4%), Chloroflexi (4.3%), and others (12.0%). Microbial α -diversity showed that the diversity of bacterial communities in the endosphere was significantly lower than that in both rhizosphere and bulk soil, which was due to the strong screening effect of plant roots on endophytic microbial colonization ( Figure 2A ), as most previous studies mentioned ( Sun et al, 2021 ; Xu et al, 2021 ). Additionally, the addition of Cu and/or PHE reduced the microbial community richness to some extent, and the influencing effects on each rhizocompartment were significantly different.…”

Section: Resultsmentioning

confidence: 69%

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Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome

et al. 2022

Front. Microbiol.

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Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 69%

Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome

et al. 2022

Front. Microbiol.

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“…It is currently an important eco‐industrial crop for the bio‐refinery industry (Heaton et al, 2009; Lewandowski et al, 2003; Zheng et al, 2019). Its strong tolerance to various environmental stresses such as heavy metal contamination (Barbosa et al, 2015; Sun et al, 2021), flooding (Mann et al, 2013), and drought (Shepherd et al, 2020) suggests a potential for phytoremediation use. More importantly, the large amount of biomass it produces can generate economic benefits.…”

Section: Introductionmentioning

confidence: 99%

Quantitative assessment of the potential for soil improvement by planting Miscanthus on saline‐alkaline soil and the underlying microbial mechanism

Zheng

et al. 2021

GCB Bioenergy

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Phytoremediation using Miscanthus is a valuable technique for the restoration of saline‐alkaline soil, but the potential is not quantified. To assess this potential, a 5 years field experiment was conducted on saline‐alkaline soils with three genotypes of Miscanthus and an unplanted control. The bulk soil (0–20‐cm depth) physicochemical properties were measured annually from 2015 to 2018, while the bacterial and fungal community structures of the rhizosphere soil were investigated by high‐throughput sequencing after 5 years under Miscanthus (2018). The results showed that Miscanthus cultivation on saline‐alkaline soil reduced soil salinization and improved soil fertility on this site. Specifically, compared with the blank control, the five‐years Miscanthus cultivation (mean of three different genotypes pooled) decreased the soil pH by 0.33 units (8.78–8.45) and electrical conductivity by 23.4 μS/cm (226.7–203.3 μS/cm), as well as increasing soil organic matter content from 18.9 to 34.9 g/kg and total potassium content from 15.2 to 18.0 g/kg. In addition, the soil improvement was more pronounced with a longer duration of growth. Miscanthus remediates saline‐alkaline soils by altering the microbial community compositional abundance rather than its diversity. The improvement is due to enrichment of beneficial bacteria leading to soil desalinization (e.g., by Gemmatimonadaceae), litter decomposition (e.g., by Chitinophagaceae), plant growth promotion (e.g., by Micrococcaceae), and the reduction of harmful fungi (e.g., Pleosporales and Chitinophagaceae). Soil pH, electrical conductivity, organic matter, and total potassium were the main physicochemical properties affecting bacterial and fungal communities. Our results quantify the soil improvement potential of Miscanthus and clarify the underlying microbial mechanisms, laying a solid foundation for further implementation of saline‐alkaline soil phytoremediation using Miscanthus. In the future, more extensive multi‐location trials are required to assess if these improvements are seen across a wide diversity of environments.

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“…The paired-sequences were merged, filtered, clustered into operational taxonomic units (OTUs, at a 97% similarity). OTUs were annotated using the Greengenes database (v. 13.8) following the previous pipelines (Sun et al, 2021). Downstream analyses for the OTU data were conducted on the MicrobiomeAnalyst platform (Dhariwal et al, 2017), including the calculation of relative abundance, alpha diversity (Shannon, observed species, Chao1 and ACE index) and beta diversity (Bray-Curtis distance matrix based principal coordinates analysis (PCoA)).…”

Section: S Rrna Gene Amplicon Sequencingmentioning

confidence: 99%

Metabolic potentials of members of the class Acidobacteriia in metal‐contaminated soils revealed by metagenomic analysis

Sun

Häggblom

et al. 2021

Environmental Microbiology

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The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriiaassociated MAGs from five additional metalcontaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.

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Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

Cited by 61 publications

References 68 publications

Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome

Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome

Quantitative assessment of the potential for soil improvement by planting Miscanthus on saline‐alkaline soil and the underlying microbial mechanism

Metabolic potentials of members of the class Acidobacteriia in metal‐contaminated soils revealed by metagenomic analysis

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