Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China

Abstract

Summary Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs‐AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome‐resolved metagenomics were performed on microbial community collected from a REEs‐AMD contaminated river. The results showed that REEs‐AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs‐dependent enzyme‐encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome‐assembled genomes covering 70.4% of identifying indicators. Genome‐centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs‐AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs‐AMD bioremediation.

'Candidatus Megaira' are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

“…One of these genomes was assembled into a single scaffold using mate-pair reads. In addition, we identified 14 previously existing MAGs in GenBank derived from previous environmental metagenome projects [60][61][62][63][64][65][66][67][68][69][70][71]. Of these, five can be considered high quality (>90 % complete, <10 % contamination).…”

Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment

“…It is worth noting that different clades were found dominant in each analysis ( Figure 3 D), and only one sequence was identified in both analyses—WP_019899159.1 ( Table 1 ). Interestingly, we detected a relatively large number of sequences of XoxF1 (in particular, based on metaproteomic analyses), whereas studies of marine and terrestrial environments indicated that XoxF4 and XoxF5 are dominant [ 33 , 46 , 48 , 49 , 50 ].…”

“…However, our study extends the existing knowledge, as the metaproteomic analysis indicated the presence of XoxF even in the order of non-methanotrophic Xanthomonadales , precisely within the aerobic heterotroph Dokdonella koreensis DS-123, described by Yoon et al (2006) [ 45 ]. Only Chen et al (2021) [ 46 ] reported that, apart from Proteobacteria , XoxF is encoded by the genome of the FCB ( Fibrobacteres , Chlorobi , and Bacteroidetes ) group, which is a superphylum.…”

‘CandidatusMegaira’ are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

“…One of these genomes was assembled into a single scaffold using mate pair reads. In addition, we identified 14 previously existing MAGs in GenBank derived from previous environmental metagenome projects [52][53][54][55][56][57][58][59][60][61][62][63]. Of these, 5 can be considered high quality (>90% complete, <10% contamination).…”