Microbial Ecology

, Volume 78, Issue 3, pp 651–664 | Cite as

Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek

  • Weimin SunEmail author
  • Enzong Xiao
  • Valdis Krumins
  • Yiran Dong
  • Baoqin Li
  • Jie Deng
  • Qi Wang
  • Tangfu Xiao
  • Jie Liu
Environmental Microbiology


Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.


Random Forest Indicator species analysis Acidimicrobiales Acid mine drainage Ecological strategies 



We thank Hanna Han and her team from Shenzhen Ecogene Co., Ltd. for their technical service.

Funding Information

This research was funded by GDAS’ Project of Science and Technology Development (2017GDASCX-0106), the National Natural Science Foundation of China (41771301, 41420104007), the High-level Leading Talent Introduction Program of GDAS (2016GDASRC-0103), the Science and Technology Planning Project of Guangdong Province (2017A070702015, 2017B030314092), GDAS’ Project of Science and Technology Development (2018GDASCX-0601, 2019GDASYL-0302006, 2019GDASYL-0301002).

Compliance with Ethical Standards

Conflict of Interest

The authors declare no conflict of interest.

Supplementary material

248_2019_1335_MOESM1_ESM.docx (811 kb)
ESM 1 (DOCX 810 kb)
248_2019_1335_MOESM2_ESM.xlsx (153 kb)
ESM 2 (XLSX 152 kb)


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Authors and Affiliations

  1. 1.Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and ManagementGuangdong Institute of Eco-environmental Science & TechnologyGuangzhouChina
  2. 2.Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and EngineeringGuangzhou UniversityGuangzhouChina
  3. 3.Department of Environmental SciencesRutgers UniversityNew BrunswickUSA
  4. 4.Institute for Genomic BiologyUniversity of IllinoisUrbanaUSA
  5. 5.School of Environmental StudiesChina University of Geosciences (Wuhan)WuhanChina
  6. 6.Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina

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