Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis

Lukhele, Thabile; Selvarajan, Ramganesh; Nyoni, Hlengilizwe; Mamba, Bhekie B.; Msagati, Titus A.M.

doi:10.1007/s00792-019-01130-7

Cited by 29 publications

(13 citation statements)

References 92 publications

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“…Although archaea of the order Thermoplasmatales are well-known inhabitants of AMD environments, including sediments, these organisms were found to be present in very low abundance and thus assumed to be unimportant ( Kock and Schippers, 2008 ; Sánchez-Andrea et al, 2011 , 2012 ; Sun et al, 2015 ; Zhang et al, 2019 ). Frequently however, the detailed information about the archaeal component is missing, or archaea were excluded from the analysis, leading to a potential underestimation of the ecological role of archaea in AMD ecosystems ( Wakelin et al, 2012 ; Lukhele et al, 2019 ). To understand the patterns of archaeal distribution in sediments of an acidic stream at Parys Mt and to assess their potential role in elemental cycling, we collected shallow sediment cores (0–20 cm depth) from the AMD stream.…”

Section: Introductionmentioning

confidence: 99%

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

et al. 2020

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Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0–20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by “E-plasma,” “A-plasma,” other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

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Section: Introductionmentioning

confidence: 99%

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

et al. 2020

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“…Similarly, different studies have unveiled the diversity of bacterial and archaeal communities that are enriched in AMD sites. Collated information of the bacterial communities dominating diverse AMD polluted environment show that Proteobacteria, Nitrospirae, Acidobacteria, Chloroflexi, and Actinobacteria are the dominant phyla (Kuang et al, 2013;Méndez-García et al, 2015;Lukhele et al, 2019;Wang et al, 2019b). Among the key dominant bacteria taxa, acidophilic proteobacterial taxa such as Acidithiobacillus spp, Leptospirillum spp., Acidiphilum spp., and Ferrovum spp, play important role chemolithotrophic metabolism of iron and sulfur under AMD environment (Kuang et al, 2013;Méndez-García et al, 2015;Wang et al, 2019b).…”

Section: Microbial Community Diversity Under Amd Habitatsmentioning

confidence: 99%

“…According to Edwards et al (2000), about 75% of AMD produced results from microbial activity. Under the extremophilic AMD environment, acidophilic microbial communities belonging to Bacteria, Archaea, and Eukarya domains dominates, with members of phylum Proteobacteria, Nitrospira, Actinobacteria, Firmicutes, and Acidobacteria being the dominant bacterial taxa (Mesa et al, 2017;Lukhele et al, 2019;Distaso et al, 2020), as well as iron/sulfur-oxidizing microbes such Leptospirillum ferrooxidans, Ferrovum, Acidothiobacillus occurring in an environmentally dependent biogeographic pattern (Kuang et al, 2013(Kuang et al, , 2016Wang et al, 2019b). In addition, a large number of rare taxa constituting a "rare biosphere" in the microbial community that may perform crucial function in AMD ecosystems have been reported (Luo et al, 2020b).…”

Section: Introductionmentioning

confidence: 99%

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Munyai

Ogola

Modise

2021

Front. Sustain. Food Syst.

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Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

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“…Amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism, lipid metabolism, and xenobiotic biodegradation and metabolism were the main pathways for metabolism, which ensured the metabolism and utilization of organic matter in the substrate. Folding, sorting, and degradation; replication and repair; transcription; and translation within genetic information processing were recovered functions, which ensured the survival of larvae in harsh environmental conditions ( Lukhele et al, 2019 ). In particular, the high relative abundance of ABC transporters, bacterial secretion system, phosphotransferase system (PTS), secretion system, and transporters within the membrane transport cluster ensured the adaptation and degradation ability of larvae.…”

Section: Discussionmentioning

confidence: 99%

Black Soldier Fly Larvae Can Effectively Degrade Oxytetracycline Bacterial Residue by Means of the Gut Bacterial Community

2021

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Antibiotic bacterial residue is a unique hazardous waste, and its safe and effective disposal has always been a concern of pharmaceutical enterprises. This report presents the effective treatment of hazardous waste—antibiotic bacterial residue—by black soldier fly larvae (larvae), oxytetracycline bacterial residue (OBR), and soya meal with mass ratios of 0:1 (soya), 1:20 (OBRlow), and 1:2 (OBRhigh), which were used as substrates for larval bioconversion. Degradation of OBR and oxytetracycline, the bacterial community, the incidence of antibiotic resistance genes (ARGs) and the bacterial function in the gut were examined. When the larvae were harvested, 70.8, 59.3, and 54.5% of the substrates had been consumed for soya, OBRlow and OBRhigh; 65.9 and 63.3% of the oxytetracycline was degraded effectively in OBRlow and OBRhigh, respectively. The larval bacterial communities were affected by OBR, abundant and various ARGs were discovered in the gut, and metabolism was the major predicted function of the gut. These findings show that OBR can be digested and converted by larvae with gut bacteria, and the larvae can be used as a bioremediation tool for the treatment of hazardous waste. Finally, the abundant ARGs in the gut deserve further attention and consideration in environmental health risk assessments.

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Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis

Cited by 29 publications

References 92 publications

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Black Soldier Fly Larvae Can Effectively Degrade Oxytetracycline Bacterial Residue by Means of the Gut Bacterial Community

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