Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars

Ye, Jun; Joseph, Stephen; Ji, Mukan; Nielsen, Shaun; Mitchell, David R. G.; Donne, Scott W.; Horvat, J.; Wang, Jianli; Munroe, Paul; Thomas, Torsten

doi:10.1038/ismej.2016.187

Cited by 123 publications

(58 citation statements)

References 91 publications

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“…The resulting sequences were used for the analysis of operational taxonomic units (OTUs), with a sequence similarity threshold of 97%. Then the Ribosomal Database Program classifier Bayesian algorithm was used to perform taxonomic analysis using representative sequences of OTUs (Ye et al 2017). To calculate alpha diversity, we calculated the Chao1 and Shannon indices (Ye et al 2017).…”

Section: Experimental Materials and Methodsmentioning

confidence: 99%

Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis

Liu

Zhou

Tao

et al. 2020

Polish Journal of Microbiology

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The root of Paris polyphylla var. yunnanensis, a famous and endangered traditional Chinese herb, has a significant medicinal value. The aim of this study was to analyze the composition and functional characteristics of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis. The 16S rRNA gene sequencing and functional prediction of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis were conducted. The Chao and Shannon indices of the bacteria in roots were significantly higher than those in stems and leaves. The dominant endophyte phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The main genera detected in roots were unclassified Cyanobacteria, Rhizobium, Flavobacterium, and Sphingobium; the main genera in stems were norank_c__Cyanobacteria, Bacillus, and Pseudomonas; the main genera in leaves were norank_c__Cyanobacteria and Rhizobium. The microbiota in roots was particularly enriched in functional categories “extracellular structures” and “cytoskeleton” compared with stems and leaves (p < 0.05). Our study reveals the structural and functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis, which aids in the scientific understanding of this plant.

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Section: Experimental Materials and Methodsmentioning

confidence: 99%

Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis

Liu

Zhou

Tao

et al. 2020

Polish Journal of Microbiology

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“…It shows some selected physicochemical properties of biochar produced under different pyrolysis temperature with different feedstock types are summarized in Table 2. The highly porous nature of biochar and its high surface area are favorable habitats for soil biota (Jaafar et al 2014(Jaafar et al , 2015Ye et al 2017). The specific area and the porosity of biochar strongly depend on the type of feedstock as well as the production temperature.…”

Section: Biochar As a Growth Promoter For Soil Biotamentioning

confidence: 99%

“…Moreover, Farrell et al (2013) reported that the application of biochar improved the soil labile C content and soil pH and altered soil microbial community structure. Nevertheless, the highly porous structure of biochar provides habitats for microorganisms to colonize, permitting their growth in the soil environment (Awad et al 2018;Lehmann et al 2011;Quilliam et al 2013;Ye et al 2017). However, neutral/negative impacts of biochar on soil biological properties have also been documented.…”

Section: Introductionmentioning

confidence: 99%

Response of microbial communities to biochar-amended soils: a critical review

Palansooriya

Wong

Hashimoto

et al. 2019

Biochar

510

160

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Application of biochar to soils changes soil physicochemical properties and stimulates the activities of soil microorganisms that influence soil quality and plant performance. Studying the response of soil microbial communities to biochar amendments is important for better understanding interactions of biochar with soil, as well as plants. However, the effect of biochar on soil microorganisms has received less attention than its influences on soil physicochemical properties. In this review, the following key questions are discussed: (i) how does biochar affect soil microbial activities, in particular soil carbon (C) mineralization, nutrient cycling, and enzyme activities? (ii) how do microorganisms respond to biochar amendment in contaminated soils? and (iii) what is the role of biochar as a growth promoter for soil microorganisms? Many studies have demonstrated that biochar-soil application enhances the soil microbial biomass with substantial changes in microbial community composition. Biochar amendment changes microbial habitats, directly or indirectly affects microbial metabolic activities, and modifies the soil microbial community in terms of their diversity and abundance. However, chemical properties of biochar, (especially pH and nutrient content), and physical properties such as pore size, pore volume, and specific surface area play significant roles in determining the efficacy of biochar on microbial performance as biochar provides suitable habitats for microorganisms. The mode of action of biochar leading to stimulation of microbial activities is complex and is influenced by the nature of biochar as well as soil conditions.

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“…The 16S rRNA gene sequence was analyzed by SILVA (SSU123) database using a confidence threshold of 70% (Cole et al, 2013;Quast et al, 2013). The subsampling was based on the minimum sample sequence with equal sequencing depth (16,175 sequences per followed by clustering) (Ye et al, 2017). Diversity metrics, that is, richness (observed species), Chao richness index, Shannon diversity index, and coverage and phylogenetic diversity were calculated based on OTU tables using mother (v.1.30.1).…”

Section: Bioinformatic Analysis Of the 16srrna Ampliconsmentioning

confidence: 99%

Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil

Liang

Song

et al. 2020

Front. Microbiol.

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Russula griseocarnosa is a wild, ectomycorrhizal, edible, and medicinal fungus with high economic value in southern China. R. griseocarnosa fruiting bodies cannot be artificially cultivated. To better understand the effects of abiotic and biotic factors on R. griseocarnosa growth, the physicochemical properties of R. griseocarnosa and its associated bacterial communities were investigated in two soil types (mycosphere and bulk soil) from Fujian, Guangdong, and Guangxi Provinces. The results revealed that the diversity, community structure, and functional characteristics of the dominant mycosphere bacteria in all geographical locations were similar. Soil pH and available nitrogen (AN) are the major factors influencing the mycosphere-soil bacterial communities' structure. The diversity of soil bacteria is decreased in R. griseocarnosa mycosphere when compared with the bulk soil. Burkholderia-Paraburkholderia, Mycobacterium, Roseiarcus, Sorangium, Acidobacterium, and Singulisphaera may also be mycorrhiza helper bacteria (MHB) of R. griseocarnosa. The functional traits related to the two-component system, bacterial secretion system, tyrosine metabolism, biosynthesis of unsaturated fatty acids, and metabolism of cofactors and vitamins were more abundant in R. griseocarnosa mycosphere soil. The mycosphere soil bacteria of R. griseocarnosa play a key role in R. griseocarnosa growth. Application of management strategies, such as N fertilizer and microbial fertilizer containing MHB, may promote the conservation, propagation promotion, and sustainable utilization of R. griseocarnosa.

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Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars

Cited by 123 publications

References 91 publications

Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis

Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis

Response of microbial communities to biochar-amended soils: a critical review

Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil

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