Bacterial community composition in the water column of a lake formed by a former uranium open pit mine

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.

Comparative analysis of the intestinal flora in type 2 diabetes and nondiabetic mice

A relationship between type 2 diabetes mellitus (T2DM) and intestinal flora has been suggested since development of analysis technology for intestinal flora. An animal model of T2DM is important for investigation of T2DM. Although there are some animal models of T2DM, a comparison of the intestinal flora of healthy animals with that of T2DM animals has not yet been reported. The intestinal flora of Tsumura Suzuki Obese Diabetes (TSOD) mice was compared with that of Tsumura, Suzuki, Non Obesity (TSNO) mice in the present study. The TSOD mice showed typical type 2 diabetes symptoms, which were high-fat diet-independent. The TSOD and the TSNO mouse models were derived from the same strain, ddY. In this study, we compared the intestinal flora of TSOD mice with that if TSNO mice at 5 and 12 weeks of age. We determined that that the number of operational taxonomic units (OTUs) was significantly higher in the cecum of TSOD mice than in that of TSNO mice. The intestinal flora of the cecum and that of the feces were similar between the TSNO and the TSOD strains. The dominant bacteria in the cecum and feces were of the phyla Firmicutes and Bacteroidetes. However, the content of some bacterial species varied between the two strains. The percentage of Lactobacillus spp. within the general intestinal flora was higher in TSOD mice than in TSNO mice. In contrast, the percentages of order Bacteroidales and family Lachnospiraceae were higher in TSNO mice than in TSOD mice. Some species were observed only in TSOD mice, such as genera Turicibacter and SMB53 (family Clostridiaceae), the percentage of which were 3.8% and 2.0%, respectively. Although further analysis of the metabolism of the individual bacteria in the intestinal flora is essential, genera Turicibacter and SMB53 may be important for the abnormal metabolism of type 2 diabetes.

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes

Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution. The results uncovered a 1,000-fold increase in the total amount of sequences harvested and a reverse relationship between trophic level and the bacterial diversity in most seasons of a year. A total of 65 phyla, 221 classes, 436 orders, 624 families, and 864 genera were identified in the study area. Delta-proteobacteria and gamma-proteobacteria prevailed in spring/summer and winter, respectively, regardless trophic conditions; meanwhile, the two classes dominated in the eutrophication and mesotrophication lake regions, respectively, but exclusively in the Fall. For LEfSe analysis, bacterial taxon that showed the strongest seasonal or spatial variation, majority had the highest abundance in spring/summer or medium eutrophication region, respectively. Pearson's correlation analysis indicated that 5 major phyla and 18 sub-phylogenetic groups showed significant correlation with trophic status. Canonical correspondence analysis further revealed that porewater NH₄⁺ -N as well as sediment TOM and NO_x -N are likely the dominant environmental factors affecting bacterial community compositions.

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.

DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies

The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.