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Zhu J, Wang HN, Tang QY, Gu MY, Zhang ZD. Composition and distribution of bacterial communities and potential radiation-resistant bacteria at different elevations in the eastern Pamirs. Front Microbiol 2024; 15:1427806. [PMID: 38962116 PMCID: PMC11220165 DOI: 10.3389/fmicb.2024.1427806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
Altitude and ultraviolet (UV) radiation may affect the community composition and distribution of microorganisms in soil ecosystems. In this study, 49 soil samples from 10 locations were collected from different elevations on the eastern Pamir Plateau and analyzed for soil microbial community structure and function using high-throughput sequencing. The results showed that soil samples from different elevations of the eastern Pamir Plateau contained 6834 OTUs in 26 phyla and 399 genera. The dominant phyla common to different elevations were Actinobacteria, Proteobacteria, Bacteroidota, Acidobacteriota, and Gemmatimonadota. The dominant genera were Rubrobacter, Sphingomonas, Nocardioides, and Solirubrobacter. Species richness increased slightly with elevation, and there were significant differences in community composition between the elevations. Elevation and UV exposure are important factors that drive changes in bacterial communities. The results of the KEGG pathway showed that drug resistance, antineoplastic, aging, replication, and repair were enhanced and then slightly decreased with increasing elevation. Bacterial communities at different elevations were rich in radiation-resistant microorganisms, and the main genera were Rubrobacter, Sphingomonas, Nocardioides, Pontibacter, and Streptomyces. The findings have shown the composition and distribution of bacterial communities at different elevations on the Eastern Pamir Plateau. Potentially radiation tolerant microbial species were also examined. The results are of considerable importance for the succession of bacterial microorganisms in the plateau region, the study of radiation tolerant bacterial germplasm resources, and the application of biofunctionality.
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Affiliation(s)
| | | | | | | | - Zhi-Dong Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
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The Study of Soil Bacterial Diversity and the Influence of Soil Physicochemical Factors in Meltwater Region of Ny-Ålesund, Arctic. Microorganisms 2022; 10:microorganisms10101913. [PMID: 36296189 PMCID: PMC9611652 DOI: 10.3390/microorganisms10101913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas.
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Manni A, Filali-Maltouf A. Diversity and bioprospecting for industrial hydrolytic enzymes of microbial communities isolated from deserted areas of south-east Morocco. AIMS Microbiol 2022; 8:5-25. [PMID: 35496990 PMCID: PMC8995190 DOI: 10.3934/microbiol.2022002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
The current study aimed to analyze bacterial communities' diversity and abundance in three different deserted areas (Merzouga, Mhamid Elghizlane, and Erg lihoud) located in Moroccan Sahara, as well as to investigate osmotolerant microorganisms producing hydrolytic enzymes. The isolates were taxonomically affiliated using 16S rRNA gene sequencing. Four different hydrolase activities (amylase, lipase, cellulase, and protease) and osmotic stress tolerance were evaluated. The phylogenetic analysis of 364 screened isolates belonged to three phyla (Firmicutes 73%, Proteobacteria 26% and Actinobacteria 1%) and 18 different genera, from Bacillus, Ornithinibacillus, Paenibacillus, Geobacillus, Pseudomonas, Acinetobacter, Agrobacterium, Arthrobacter, Paenarthrobacter, Enterobacter, Staphylococcus, Erwinia, Herbasprillum, Ocuria, Massilia, Planomicrobium, Hodococcus, and Stenotrophomonas. The results detected a high proportion of osmotolerant and enzymes producing bacteria, many isolates can tolerate up to 55 °C (40%, 28%, and 30% in Merzouga, Mhamid Elghizlane, and Erg lihoudi, respectively). Meanwhile, the salinity tolerance reached 12% in some isolates with different proportions in each site, 29% in Merzouga, 24% in Mhamid Elghizlane, and 9% in Erg lihoudi. Furthermore, the enzymatic tests showed the presence of an amylolytic, lipolytic, cellulolytic, proteolytic activities in 20%, 31%, 63% and 72% of total strains, respectively. As a result, the present study is thus a preliminary yet critical step towards identifying the best bacterial candidates for further biotechnological applications.
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Liu Z, Yang Y, Ji S, Dong D, Li Y, Wang M, Han L, Chen X. Effects of Elevation and Distance from Highway on the Abundance and Community Structure of Bacteria in Soil along Qinghai-Tibet Highway. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413137. [PMID: 34948747 PMCID: PMC8701971 DOI: 10.3390/ijerph182413137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/27/2021] [Accepted: 12/04/2021] [Indexed: 11/21/2022]
Abstract
In recent years, highway construction in the Qinghai-Tibet Plateau (QTP) has developed rapidly. When the highway passes through grassland, the soil, vegetation, and ecological environment along the line are disturbed. However, the impact on soil bacteria is still unclear. Soil bacteria play an important role in the ecological environment. The Qinghai-Tibet Highway (QTH) was selected as the research object to explore the changes in bacterial community structure, vegetation, soil, and other indicators. The results showed that the highway-related activities increased the degradation of vegetation along the road, significantly changed the physical and chemical properties of soil, and caused heavy metal pollution. These environmental factors affected the diversity and community structure of soil bacteria. This kind of disturbance shows a trend of gradually increasing from near to far from the highway. Gemmatimonas, Terrimonas, Nitrospira and Bacillus are more tolerant to environmental changes along the highway, while Barnesiella, and Blastococcus are more sensitive. The content of nitrate decreased and the content of ammonium nitrogen increased in the disturbed area, increasing the abundance of nitrifying bacteria. Therefore, the main factor of the disturbance of the QTH on the grassland is the decline of soil nutrient content, and the supplement of soil nutrients such as carbon and nitrogen should be taken into account in the process of ecological restoration of grassland along the line.
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Affiliation(s)
- Zhuocheng Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Yangang Yang
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Shuangxuan Ji
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Yinruizhi Li
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Mengdi Wang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Correspondence: (L.H.); (X.C.)
| | - Xueping Chen
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
- Correspondence: (L.H.); (X.C.)
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Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies. Extremophiles 2021; 26:3. [PMID: 34878610 DOI: 10.1007/s00792-021-01252-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022]
Abstract
Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.
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Luo Y, Liu F, Ren J, Zhu J, Luo X, Xiang Y. Effects of dominant plant growth on the nutrient composition and bacterial community structure of manganese residues. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 24:525-535. [PMID: 34382471 DOI: 10.1080/15226514.2021.1957769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The rhizospheres of three dominant plant species (Miscanthus floridulus, Buddleja lindleyana, and Erigeron annuus) growing in manganese residue disposal sites in eastern Guizhou Province, China, were analyzed to study the effects of plant growth on the nutrient levels and bacterial community structure of two types of manganese residues. The results showed that the growth of the three species improved the nutritional composition of manganese residues; the available nitrogen (AN) contents of the manganese mine residue significantly increased by 29.56-60.78% while the available phosphorus (AP) contents of the electrolytic manganese residue significantly increased by 30.24-44.41% compared to those in unvegetated manganese residue. The diversity of the bacterial community in the manganese mine residue increased significantly due to plant growth. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla in both manganese residues. Sphingomonas and GP6 were the dominant bacterial genera. The relative abundance of the Firmicutes phylum was significantly higher in the manganese mine residue than in the control and that of the Thiobacillus genus was lower, which indicated improvements in the microenvironment. Correlation analysis showed that OM and AN were the main nutrient factors affecting the bacterial community structure in the manganese mine residue.Novelty statement At present, research on the phytoremediation of manganese residue disposal sites focuses mostly on the investigation of different plant types and their heavy metal accumulation and transformation characteristics. However, comparative studies of the differences in growth matrix characteristics between plant growth areas and exposed areas are lacking. In addition, dominant plant species are regionally distributed. The previous studies were mostly concentrated in Chongqing, Guangxi, and Hunan in China. The eastern region of Guizhou Province is located in the "Manganese Triangle" area of China, where the manganese resources account for about 50% of the national total. There is no report on the phytoremediation of manganese residue disposal sites in this region. Therefore, the rhizospheres of three dominant plant species (Miscanthus floridulus, Buddleja lindleyana, and Erigeron annuus) growing in manganese residue disposal sites in eastern Guizhou Province, China, were analyzed to study the effects of plant growth on the nutrient levels and bacterial community structure of two types of manganese residues (manganese mine residue and electrolytic manganese residue). This study could provide useful theoretical information to benefit the ecological restoration of manganese residue disposal sites.
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Affiliation(s)
- Yang Luo
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Fang Liu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
| | - Jun Ren
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Jian Zhu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
| | - Xuqiang Luo
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Yangzhou Xiang
- School of Geography and Resources, Guizhou Education University, Guiyang, China
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