Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan
Abstract
:1. Introduction
2. Materials and Methods
2.1. River Sediment Sample Collection and Processing
2.2. Chemical Analysis of Sediments
2.3. Testing of Microbial DNA in Sediments
2.3.1. DNA Extraction and Shotgun Sequencing
2.3.2. Shotgun Sequencing Data Analysis
2.3.3. Identification of Microbial Resistance Genes
2.4. Statistical Analysis
3. Results
3.1. Chemical Characterization of Sediments
Concentration of Cr, Cu, Zn, Pb, and Cd in River Sediments and Water
3.2. Taxonomic Profile of Sediment Samples
Abundance of Antibiotic Resistance Genes
3.3. Principal Component Analysis (PCA) of Chemical Variables and Abundance of Resistance Genes
4. Discussion
5. Conclusions
- Ten samples of riverbed sediments taken from different sites in the East Kazakhstan region considerably contrasted in their physicochemical characteristics and contamination with HMes. The highest HMe concentrations were detected in Ridder City (K8 and K9) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (K4). These samples were also characterized by the highest total number of identified functional gene families, including those related to Zn, Cu, Ni, Co, and Cd.
- The prevalence of Proteobacteria and Actinobacteria at the phylum level was shown in all ten samples examined in this study. At lower taxonomic ranks, the tested sediments differed in dominant bacteria. The data on the prevalence of bacteria taxa in river sediments at historically contaminated sites represent an important tool for the further investigation of microbial multi-resistance toward HMe, as well as other substances (e.g., antibiotics).
- The most HMe-contaminated sediments (i.e., K4, K8, K9) were characterized by a considerably lower number of ARGs compared with K1. Apparently, sampling site K1—situated in Ust-Kamenogorsk in Irtysh River, 2 km below the confluence with the Ulba River—may be heavily influenced by other anthropogenic factors, not by HMe contamination.
- A lack of data on the concentration of other pollutants (e.g., other metals, hydrocarbons, S- and F-containing molecules, etc.), seasonal variables, the spatial distribution of contamination, and other factors means that we might be underestimating the selective pressure of living surrounding on the microbial community structure in riverbed sediments. Further study is needed for a deeper understanding of the interplay between mining activities, urbanization, environmental changes, and the response of microorganisms as the main inhabitants among benthic organisms. New knowledge in this field will provide essential insights into sustainable river management in the context of intensive mining and metallurgy activities.
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Name | Number of Raw Reads | Classified Reads | Chordate Reads, % | Bacterial Reads, % | Viral Reads, % | Fungal Reads, % | Protozoan Reads, % |
---|---|---|---|---|---|---|---|
K1 | 34492563 | 13.50% | 1.85 × 10−5 | 13.30% | 2.71 × 10−5 | 2.01 × 10−4 | 2.26 × 10−7 |
K2 | 26690851 | 6.07% | 5.21 × 10−6 | 5.97% | 5.73 × 10−6 | 1.39 × 10−5 | 8.62 × 10−7 |
K3 | 27166997 | 4.09% | 1.69 × 10−5 | 3.99% | 1.33 × 10−6 | 1.17 × 10−5 | 4.79 × 10−7 |
K4 | 41615524 | 3.79% | 1.56 × 10−6 | 3.69% | 9.61 × 10−7 | 4.81 × 10−6 | 5.77 × 10−7 |
K5 | 14414917 | 4.21% | 2.15 × 10−6 | 4.10% | 5.55 × 10−7 | 6.04 × 10−6 | 2.77 × 10−7 |
K6 | 28902876 | 5.25% | 3.81 × 10−6 | 5.12% | 1.28 × 10−6 | 2.96 × 10−5 | 9.34 × 10−7 |
K7 | 39748441 | 4.00% | 7.45 × 10−6 | 3.89% | 3.47 × 10−6 | 1.73 × 10−5 | 7.80 × 10−7 |
K8 | 23419659 | 4.53% | 3.83 × 10−5 | 4.42% | 3.33 × 10−6 | 1.67 × 10−5 | 7.69 × 10−7 |
K9 | 26108461 | 6.09% | 1.40 × 10−5 | 5.98% | 1.11 × 10−6 | 1.18 × 10−5 | 4.98 × 10−7 |
K10 | 41973872 | 4.53% | 4.19 × 10−6 | 4.41% | 1.83 × 10−6 | 1.71 × 10−5 | 7.86 × 10−7 |
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Sample No. | Geographical Coordinates of Sampling Sites | Name of the Location | Description of Sampling Sites |
---|---|---|---|
K1 | 49°57′30.6″ N 82°34′16.7″ E | Ust-Kamenogorsk, 070000, Kazakhstan | Irtysh River 2 km below the confluence with the Ulba River (Samal district) |
K2 | 49°55′36.3″ N 82°40′10.6″ E | Irtysh River, 3 km above the Pionersky water intake (Ablaketka District) | |
K3 | 49°57′15.0″ N 82°36′45.0″ E | Ulba River, Ust-Kamenogorsk, within the city; 1 km above the mouth of the Ulba River; 0.36 km below the Ulbinsky bridge; right bank | |
K4 | 49°53′29.0″ N 82°42′12.0″ E | Irtysh River, Ust-Kamenogorsk, within the city; 0.8 km below the dam of the Ust-Kamenogorsk hydroelectric power station; at the water post site; right bank | |
K5 | 49°55′37.0″ N 82°40′10.0″ E | Irtysh River, 0.5 km below the wastewater discharge of the capacitor plant, 0.5 km above the railway bridge, right bank | |
K6 | 50°15′16.0″ N 82°21′47.0″ E | Glubokoye District, 070000, Kazakhstan | Krasnoyarka River, within Altai Village; 60 m below the hydraulic structure (dam); 24 km above the mouth of the Krasnoyarka River; right bank |
K7 | 50°14′50.0″ N 82°14′39.0″ E | Predgornoje, 070000, Kazakhstan | Krasnoyarka River, within the boundaries of the village of Predgornoye; 3.5 km above the mouth; at the water station site; right bank |
K8 | 50°21′26.0″ N 83°28′53.0″ E | Ridder, 070000, Kazakhstan | Tikhaya River, 0.1 km above the technological road bridge; 0.17 km above the confluence of the Bezymianny stream; left bank |
K9 | 50°19′17.0″ N 83°25′52.73″ E | Tikhaya River, 0.23 km below the hydraulic structure (dam); 8 km above the mouth of the Tikhaya River; left bank | |
K10 | 49°37′10.0″ N 83°26′25.4″ E | Bukhtarma Reservoir, 070000, Kazakhstan | Bukhtarma Reservoir |
Sample | OM, % | P2O5, mg kg−1 | Ntot, % | Ctot, % | C/N Ratio |
---|---|---|---|---|---|
K1 | 1.52 | 45.70 ± 0.71 | 0.029 ± 0.003 | 0.696 ± 0.177 | 23.98 |
K2 | 1.02 | 49.25 ± 1.48 | 0.023 ± 0.012 | 0.254 ± 0.179 | 11.27 |
K3 | 2.27 | 62.30 ± 1.27 | 0.064 ± 0.012 | 0.703 ± 0.045 | 11.07 |
K4 | 2.07 | 45.60 ±5.94 | 0.036 ± 0.022 | 0.730 ± 0.224 | 20.55 |
K5 | 0.70 | 25.35 ± 1.34 | 0.011 ± 0.002 | 0.098 ± 0.023 | 9.33 |
K6 | 3.92 | 38.30 ± 1.41 | 0.142 ± 0.002 | 2.510 ± 0.260 | 17.74 |
K7 | 6.85 | 13.55 ± 0.49 | 0.146 ± 0.001 | 2.935 ± 0.005 | 20.17 |
K8 | 3.76 | 40.55 ± 0.49 | 0.082 ± 0.001 | 2.384 ± 0.547 | 29.25 |
K9 * | 0.63 | 8.90 ± 0.00 | 0.019 ± 0.003 | 0.377 ± 0.042 | 20.20 |
K10 * | 0.64 | 37.10 ± 0.00 | 0.022 ± 0.006 | 0.123 ± 0.002 | 5.51 |
Sample | Cr | Cu | Zn | Cd | Pb |
---|---|---|---|---|---|
mg kg−1 | mg kg−1 | mg kg−1 | mg kg−1 | mg kg−1 | |
K1 | 23.41 | 8.81 | 33.87 | 3.23 | 5.56 |
K2 | 16.67 | 14.87 | 12.19 | 0.25 | 6.01 |
K3 | 20.59 | 19.56 | 22.58 | 0.41 | 8.66 |
K4 | 35.26 | 16.10 | 42.04 | 7.47 | 13.90 |
K5 | 21.72 | 15.92 | 18.35 | 0.46 | 5.69 |
K6 | 18.27 | 16.63 | 16.83 | 0.34 | 5.61 |
K7 | 11.58 | 6.61 | 27.67 | 0.46 | 5.75 |
K8 | 23.28 | 25.11 | 67.35 | 8.53 | 32.00 |
K9 | 24.26 | 23.73 | 53.04 | 5.12 | 36.70 |
K10 | 22.67 | 17.03 | 24.70 | 0.24 | 4.08 |
Species | K1 | K2 | K3 | K4 | K5 | K6 | K7 | K8 | K9 | K10 |
---|---|---|---|---|---|---|---|---|---|---|
Acidovorax sp. JMULE5 | 0.04 | 0.02 | 0.23 | 1.66 | 1.23 | 0.96 | 10.08 | 0.46 | 2.00 | 0.11 |
Acinetobacter baumannii | 0.14 | 3.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.09 | 0.00 | 0.02 |
Acinetobacter johnsonii | 14.07 | 6.99 | 0.02 | 0.03 | 0.01 | 0.02 | 0.06 | 0.28 | 0.01 | 0.07 |
Acinetobacter lwoffii | 15.74 | 1.63 | 0.02 | 0.03 | 0.02 | 0.07 | 0.03 | 0.04 | 0.02 | 0.04 |
Acinetobacter sp. ACNIH2 | 3.50 | 2.61 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 |
Actinoplanes derwentensis | 0.00 | 0.00 | 0.15 | 0.00 | 0.00 | 0.15 | 0.03 | 14.06 | 0.00 | 0.00 |
Aeromonas salmonicida | 0.02 | 0.02 | 0.02 | 6.88 | 0.24 | 0.70 | 0.03 | 0.06 | 0.00 | 0.08 |
Aeromonas sp. CU5 | 0.00 | 0.12 | 0.07 | 34.73 | 0.17 | 0.09 | 0.01 | 0.01 | 0.00 | 0.43 |
Aeromonas veronii | 0.01 | 0.05 | 0.04 | 9.33 | 0.08 | 0.11 | 0.02 | 0.10 | 0.00 | 0.17 |
Archangium gephyra | 0.52 | 0.00 | 6.00 | 0.00 | 0.66 | 5.70 | 0.01 | 0.01 | 0.02 | 3.87 |
Arthrobacter sp. FB24 | 0.44 | 2.21 | 0.56 | 0.04 | 0.15 | 0.01 | 0.02 | 0.04 | 1.07 | 6.02 |
Bosea sp. RAC05 | 0.02 | 1.79 | 9.59 | 0.02 | 0.69 | 0.55 | 0.13 | 1.52 | 1.09 | 0.62 |
Burkholderiales bacterium JOSHI_001 | 0.03 | 0.09 | 0.63 | 2.37 | 2.60 | 0.69 | 1.04 | 0.70 | 0.95 | 6.40 |
Buttiauxella sp. 3AFRM03 | 3.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 |
Caulobacteraceae bacterium OTSz_A_272 | 0.00 | 0.07 | 0.39 | 0.72 | 0.39 | 0.20 | 0.18 | 0.14 | 0.61 | 0.86 |
Exiguobacterium mexicanum | 3.96 | 0.20 | 0.06 | 0.00 | 0.02 | 0.64 | 0.02 | 0.00 | 0.00 | 0.02 |
Flavobacterium sp. Sr18 | 0.44 | 7.67 | 0.05 | 0.30 | 0.22 | 0.04 | 0.54 | 0.29 | 0.11 | 2.37 |
Gemmatimonas phototrophica | 0.01 | 1.23 | 8.31 | 0.03 | 0.47 | 1.29 | 2.72 | 2.30 | 0.80 | 1.05 |
Hydrogenophaga sp. RAC07 | 0.01 | 0.03 | 0.44 | 0.31 | 7.48 | 0.14 | 1.35 | 1.50 | 5.20 | 0.78 |
Microbacteriaceae bacterium WY83 | 0.21 | 0.04 | 0.24 | 0.00 | 5.00 | 0.03 | 1.45 | 0.22 | 4.27 | 0.01 |
Microcoleus sp. PCC 7113 | 0.00 | 0.00 | 2.41 | 0.00 | 0.00 | 3.81 | 0.00 | 0.00 | 0.04 | 0.01 |
Micromonospora zamorensis | 0.02 | 0.13 | 0.05 | 0.02 | 0.01 | 3.44 | 0.29 | 0.06 | 0.05 | 0.01 |
Microvirga ossetica | 0.12 | 0.06 | 1.33 | 0.16 | 0.10 | 17.81 | 0.87 | 0.19 | 0.06 | 0.02 |
Modestobacter marinus | 0.01 | 0.01 | 0.48 | 0.02 | 0.01 | 7.83 | 0.05 | 0.07 | 0.50 | 0.09 |
Mycolicibacterium arabiense | 0.01 | 0.01 | 0.13 | 0.00 | 0.03 | 4.91 | 0.09 | 0.05 | 0.02 | 0.01 |
Nitrosomonas sp. Is79A3 | 0.01 | 0.09 | 0.81 | 0.18 | 4.72 | 0.41 | 0.64 | 3.24 | 0.55 | 2.50 |
Nitrospira defluvii | 0.07 | 0.06 | 0.75 | 0.13 | 1.46 | 1.13 | 10.10 | 7.20 | 1.93 | 0.38 |
Novosphingobium ginsenosidimutans | 0.09 | 4.50 | 6.24 | 0.15 | 1.44 | 0.43 | 2.44 | 1.06 | 0.13 | 2.15 |
Opitutus sp. GAS368 | 0.00 | 0.25 | 2.11 | 0.46 | 0.91 | 1.03 | 11.79 | 1.65 | 3.39 | 3.06 |
Pantoea agglomerans | 10.81 | 0.07 | 0.02 | 0.02 | 0.02 | 0.25 | 0.06 | 0.04 | 0.00 | 0.02 |
Planctomycetes bacterium ETA_A1 | 0.14 | 0.47 | 4.08 | 0.34 | 1.77 | 3.15 | 2.87 | 1.31 | 1.29 | 8.19 |
Planctomycetes bacterium I41 | 0.07 | 1.66 | 9.53 | 0.10 | 0.63 | 0.34 | 0.17 | 0.31 | 1.59 | 7.13 |
Pseudomonas entomophila | 0.01 | 3.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.01 |
Pseudomonas putida | 0.58 | 4.82 | 0.07 | 0.03 | 0.04 | 0.04 | 0.05 | 0.13 | 1.50 | 0.05 |
Pseudomonas silesiensis | 12.19 | 11.56 | 0.02 | 0.34 | 0.23 | 0.06 | 0.20 | 0.02 | 3.76 | 0.07 |
Pseudomonas sp. UW4 | 0.06 | 0.25 | 0.01 | 0.52 | 0.00 | 0.02 | 0.05 | 0.01 | 8.92 | 0.01 |
Pseudomonas umsongensis | 0.94 | 0.77 | 0.01 | 0.03 | 0.13 | 0.01 | 0.02 | 0.03 | 7.04 | 0.01 |
Rhodoferax sp. BAB1 | 0.01 | 0.92 | 0.40 | 0.02 | 5.79 | 2.93 | 0.51 | 0.40 | 2.45 | 1.78 |
Serpentinomonas mccroryi | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 3.99 | 0.01 | 0.02 |
Sphingosinicella sp. BN140058 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 4.10 | 0.00 | 0.00 | 0.01 | 0.00 |
Sulfuricaulis limicola | 0.01 | 0.19 | 0.19 | 0.04 | 0.20 | 0.03 | 0.52 | 0.09 | 0.02 | 5.12 |
Tabrizicola piscis | 0.53 | 0.53 | 1.95 | 0.15 | 35.25 | 0.92 | 1.51 | 0.89 | 0.82 | 1.09 |
Undibacterium parvum | 0.00 | 0.04 | 0.04 | 19.35 | 0.17 | 0.00 | 0.02 | 0.21 | 0.05 | 0.13 |
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Muter, O.; Gudrā, D.; Daumova, G.; Idrisheva, Z.; Rakhymberdina, M.; Tabors, G.; Dirnēna, B.; Dobkeviča, L.; Petrova, O.; Apshikur, B.; et al. Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan. Microorganisms 2024, 12, 246. https://doi.org/10.3390/microorganisms12020246
Muter O, Gudrā D, Daumova G, Idrisheva Z, Rakhymberdina M, Tabors G, Dirnēna B, Dobkeviča L, Petrova O, Apshikur B, et al. Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan. Microorganisms. 2024; 12(2):246. https://doi.org/10.3390/microorganisms12020246
Chicago/Turabian StyleMuter, Olga, Dita Gudrā, Gulzhan Daumova, Zhanat Idrisheva, Marzhan Rakhymberdina, Guntis Tabors, Baiba Dirnēna, Linda Dobkeviča, Olga Petrova, Baitak Apshikur, and et al. 2024. "Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan" Microorganisms 12, no. 2: 246. https://doi.org/10.3390/microorganisms12020246