1
|
Iqbal A, Ligeng J, Mo Z, Adnan M, Lal R, Zaman M, Usman S, Hua T, Imran M, Pan SG, Qi JY, Duan M, Gu Q, Tang X. Substation of vermicompost mitigates Cd toxicity, improves rice yields and restores bacterial community in a Cd-contaminated soil in Southern China. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133118. [PMID: 38101017 DOI: 10.1016/j.jhazmat.2023.133118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Cadmium (Cd) contamination in agricultural soil is a global concern for soil health and food sustainability because it can cause Cd accumulation in cereal grains. An in-situ stabilizing technology (using organic amendments) has been widely used for Cd remediation in arable lands. Therefore, the current study examined the influence of vermicompost (VC) on soil biochemical traits, bacterial community diversity and composition, Cd uptake and accumulation in rice plants and grain yield in a Cd-contaminated soil during the late growing season in 2022. Different doses of VC (i.e., V1 = 0 t ha-1, V2 = 3 t ha-1 and V3 = 6 t ha-1) and two concentrations of Cd (i.e., Cd1 = 0 and Cd2 = 50 mg Cd Kg-1 were used. We performed high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize soil bacterial communities. The addition of VC considerably affected the diversity and composition of the soil bacterial community; and increased the relative abundance of phyla Chloroflexi, Proteobacteria, Acidobacteriota, Plantomycetota, Gemmatimonadota, Patescibacteria and Firmicute. In addition, VC application, particularly High VC treatment, exhibited the highest bacterial diversity and richness (i.e., Simpson, Shannon, ACE, and Chao 1 indexes) of all treatments. Similarly, the VC application increased the soil chemical traits, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), total potassium (TK), total phosphorous (TP) and enzyme activities (i.e., acid phosphatase, catalase, urease and invertase) compared to non-VC treated soil under Cd stress. The average increase in SOC, TN, AN, TK and TP were 5.75%, 41.15%, 18.51%, 12.31%, 25.45% and 29.67%, respectively, in the High VC treatment (Pos-Cd + VC3) compared with Cd stressed soil. Redundancy analysis revealed that the leading bacterial phyla were associated with SOC, AN, TN, TP and pH, although the relative abundance of Firmicutes, Proteobacteria, Bacteroidata, and Acidobacteria on a phylum basis and Actinobacteria, Gammaproteobacteria and Myxococcia on a class basis, were highly correlated with soil environmental factors. Moreover, the VC application counteracted the adverse effects of Cd on plants and significantly reduced the Cd uptake and accumulation in rice organs, such as roots, stem + leaves and grain under Cd stress conditions. Similarly, applying VC significantly increased the fragrant rice grain yield and yield traits under Cd toxicity. The correlation analysis showed that the increased soil quantities traits were crucial in obtaining high rice grain yield. Generally, the findings of this research demonstrate that the application of VC in paddy fields could be useful for growers in Southern China by sustainably enhancing soil functionality and crop production.
Collapse
Affiliation(s)
- Anas Iqbal
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, Guangxi University, Nanning 530004, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China; CFAES Rattan Lal Center for Carbon Management and Sequestration, The Ohio State University, 210 Kottman Hall, 2021 Coffey Rd, Columbus, OH 43210, USA; Departmetn of Entomology, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Jiang Ligeng
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Zhaowen Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Muhammad Adnan
- CFAES Rattan Lal Center for Carbon Management and Sequestration, The Ohio State University, 210 Kottman Hall, 2021 Coffey Rd, Columbus, OH 43210, USA
| | - Rattan Lal
- CFAES Rattan Lal Center for Carbon Management and Sequestration, The Ohio State University, 210 Kottman Hall, 2021 Coffey Rd, Columbus, OH 43210, USA
| | - Maid Zaman
- Departmetn of Entomology, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Sayed Usman
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Tian Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Muhammad Imran
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Sheng-Gang Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Jian-Ying Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Meiyang Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Qichang Gu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Xiangru Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China.
| |
Collapse
|
2
|
Liu Q, Bai C, Zhang Z, Yin X, Lin W, Huang Y, Yao L. Straw incorporation induces rice straighthead disease in As-contaminated paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:167383. [PMID: 37758142 DOI: 10.1016/j.scitotenv.2023.167383] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/06/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Rice straw incorporation is globally recognized as a viable alternative to incineration. However, it might lead to arsenic (As) methylation in soils, resulting in increased accumulation of methylated As in rice plants, potentially contributing to the emergence of rice straighthead disease. To evaluate the effect of straw incorporation on the As transformation in the paddy field system, we conducted a pot experiment for rice cultivation in two paddy soils with different As background levels and also characterized the response of the soil microbial community to straw incorporation. The results showed that straw incorporation elevated the total and methylated As concentration within the soil solution and rice plants, which in turn reduced rice seed setting rate and yield, and caused straighthead disorder in rice cultivated in soils with high As levels. 16S rRNA-based sequencing demonstrated reduced abundance and diversity of microorganisms upon adding straw. Notably, the dominant phylum, Bacteroidetes, exhibited a significant increase in abundance due to straw integration, while the abundance of Proteobacteria and Acidobacteria decreased. At the family level, the prevalence of Rikenellaceae increased only in soils contaminated with As following straw incorporation. Redundancy analysis showed positive associations between Rikenellaceae and levels of methylated As present in both soil porewater and rice husks, suggesting a potentially pivotal role of Rikenellaceae in the As methylation process after straw integration. These findings collectively emphasize that including straw can reshape the soil's microbial community and amplify As methylation in the soil, thereby promoting the uptake and accumulation of methylated As in rice and inducing straighthead disease in As-contaminated soil.
Collapse
Affiliation(s)
- Qinghui Liu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Cuihua Bai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Guangzhou 510642, China.
| | - Zhijun Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xueying Yin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Wanting Lin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yinghui Huang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Lixian Yao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Guangzhou 510642, China.
| |
Collapse
|
3
|
Tang X, Zhang M, Fang Z, Yang Q, Zhang W, Zhou J, Zhao B, Fan T, Wang C, Zhang C, Xia Y, Zheng Y. Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau. FEMS Microbiol Ecol 2023; 99:fiad117. [PMID: 37766397 DOI: 10.1093/femsec/fiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.
Collapse
Affiliation(s)
- Xiaotong Tang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhengkun Fang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wan Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxing Zhou
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tongyu Fan
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Congzhen Wang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Zheng
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| |
Collapse
|
4
|
Xu D, Yu X, Chen J, Li X, Chen J, Li J. Effects of compost as a soil amendment on bacterial community diversity in saline-alkali soil. Front Microbiol 2023; 14:1253415. [PMID: 37829448 PMCID: PMC10565496 DOI: 10.3389/fmicb.2023.1253415] [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: 07/05/2023] [Accepted: 08/23/2023] [Indexed: 10/14/2023] Open
Abstract
Introduction Soil salinization poses a worldwide challenge that hampers agricultural productivity. Methods Employing high-throughput sequencing technology, we conducted an investigation to examine the impact of compost on the diversity of bacterial communities in saline soils. Our study focused on exploring the diversity of bacterial communities in the inter-root soil of plants following composting and the subsequent addition of compost to saline soils. Results Compared to the initial composting stage, Alpha diversity results showed a greater diversity of bacteria during the rot stage. The germination index reaches 90% and the compost reaches maturity. The main bacterial genera in compost maturation stage are Flavobacterium, Saccharomonospora, Luteimonas and Streptomyces. Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla in the soil after the addition of compost. The application of compost has increased the abundance of Actinobacteria and Chloroflexi by 7.6 and 6.6%, respectively, but decreased the abundance of Firmicutes from 25.12 to 18.77%. Redundancy analysis revealed that soil factors pH, solid urease, organic matter, and total nitrogen were closely related to bacterial communities. Discussion The addition of compost effectively reduced soil pH and increased soil enzyme activity and organic matter content. An analysis of this study provides theoretical support for compost's use as a saline soil amendment.
Collapse
Affiliation(s)
- Daolong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowen Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Minister of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jin Chen
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiufen Li
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - JiangHua Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
5
|
Yang Z, Lou Y, Yan X, Pan H, Wang H, Yang Q, Sun Y, Zhuge Y. The Microbiome and Antibiotic Resistome in Soil under Biodegradable Composite Carbon Source Amendment. J Xenobiot 2023; 13:424-438. [PMID: 37606424 PMCID: PMC10443276 DOI: 10.3390/jox13030027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
The decomposition of biodegradable composite carbon sources generates a large amount of biodegradable microplastics, which may not only furnish microbial denitrification, but might also pose potential environmental risks. In the present study, the effects of different dosages of a biodegradable composite carbon source on the microbial communities, the nitrogen metabolic pathways and the antibiotic resistome were explored through Illumina MiSeq sequencing analysis and metagenomic analysis. The results of partial least-square discriminant analysis (PLS-DA) and analysis of similarity (ANOSIM) demonstrated that the response of the bacterial community to a biodegradable composite carbon source was more obvious than the fungal community. The application of biodegradable microplastics diminished the complexity of the microbial communities to some extent and obviously stimulated denitrification. Antibiotics resistance gene (ARG) dispersal was not evidently accelerated after the addition of biodegradable composite carbon source. Lysobacter, Methylobacillus, Phyllobacterium, Sinorhizobium, Sphingomonas from Proteobacteria and Actinomadura, Agromyces, Gaiella and Micromonospora from Actinobacteria were the major ARG hosts. Overall, the addition of a biodegradable composite carbon source shaped microbial communities and their antibiotic resistance profiles in this study.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yuping Zhuge
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (Z.Y.); (Y.L.); (X.Y.); (H.P.); (H.W.); (Q.Y.); (Y.S.)
| |
Collapse
|
6
|
Amores-Arrocha H, Asamoah-Asare AKB, Opio J, Martin A, Cuthbertson L, Bradford HR, Avila-Jimenez ML, Pearce DA. Analysis of Bacterial Communities around the Adventdalen Landfill Site in Svalbard. Microorganisms 2023; 11:microorganisms11041093. [PMID: 37110516 PMCID: PMC10146328 DOI: 10.3390/microorganisms11041093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Ecosystems are often resilient enough to fully recover following a natural disturbance, or to transform into a new equilibrium favourable to the surrounding flora and fauna. However, at a local level, whether this transformation will be beneficial or not depends strongly on the level of disturbance and the available mechanisms for recovery. The Arctic, however, provides a potentially extreme environment for microbial growth and this is reflected in the microbial biodiversity, the in-situ growth rates, the biogeochemical cycling and its sensitivity to environmental change. In this study, we evaluated the current microbial biodiversity and environmental conditions around the landfill site in Adventdalen, Svalbard to identify differences across bacterial communities that might promote or accelerate naturally occurring environmental recovery. Landfill sites can induce changes in the local environment through the input of exogenous chemicals (both organic and inorganic) and microorganisms. Leachate can flow with run-off from the primary location of the landfill site due to rain, snow or ice melt and spread material into soils surrounding the site. In this study we found a strong effect of the landfill site on the bacterial diversity in the local landscape. Intervention is highly desirable to enhance the environment and improve the restoration by subtly altering the conditions at the site (such as the pH or drainage courses) and by encouraging specific groups of naturally occurring indigenous microorganisms to bioremediate the site.
Collapse
Affiliation(s)
- Hermi Amores-Arrocha
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | - Alex K B Asamoah-Asare
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | - Joyce Opio
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | - Alex Martin
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | - Lewis Cuthbertson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | - Hannah R Bradford
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| | | | - David A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
| |
Collapse
|
7
|
Romanowicz KJ, Kling GW. Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra. Environ Microbiol 2022; 24:6220-6237. [PMID: 36135820 PMCID: PMC10092252 DOI: 10.1111/1462-2920.16218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi-decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active-layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.
Collapse
Affiliation(s)
- Karl J Romanowicz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - George W Kling
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
8
|
Zaitseva S, Badmaev N, Kozyreva L, Dambaev V, Barkhutova D. Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia). Microorganisms 2022; 10:2202. [PMID: 36363794 PMCID: PMC9695985 DOI: 10.3390/microorganisms10112202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2023] Open
Abstract
Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.
Collapse
Affiliation(s)
- Svetlana Zaitseva
- Institute of General and Experimental Biology SD RAS, 670047 Ulan-Ude, Russia
| | | | | | | | | |
Collapse
|
9
|
Tagg AS, Sperlea T, Labrenz M, Harrison JP, Ojeda JJ, Sapp M. Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth. Microorganisms 2022; 10:microorganisms10091775. [PMID: 36144377 PMCID: PMC9506493 DOI: 10.3390/microorganisms10091775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.
Collapse
Affiliation(s)
- Alexander S. Tagg
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
- Correspondence:
| | - Theodor Sperlea
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Matthias Labrenz
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Jesse P. Harrison
- CSC—IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Jesús J. Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
| | - Melanie Sapp
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| |
Collapse
|
10
|
Li X, Cui Y, Ma D, Song D, Liu L. Vertical distribution of bacterial community diversity in the Greater Khingan Mountain permafrost region. Ecol Evol 2022; 12:e9106. [PMID: 35845356 PMCID: PMC9272067 DOI: 10.1002/ece3.9106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Soil microorganisms are crucial contributors to the function of permafrost ecosystems, as well as the regulation of biogeochemical cycles. However, little is known about the distribution patterns and drivers of high‐latitude permafrost microbial communities subject to climate change and human activities. In this study, the vertical distribution patterns of soil bacterial communities in the Greater Khingan Mountain permafrost region were systematically analyzed via Illumina Miseq high‐throughput sequencing. Bacterial diversity in the active layer was significantly higher than in the permafrost layer. Principal coordinate analysis (PCoA) indicated that the bacterial community structure in the active layer and the permafrost layer was completely separated. Permutational multivariate analysis of variance (PERMANOVA) detected statistically significant differentiation across the different depths. The relative abundance of the dominant phyla Chloroflexi (17.92%–52.79%) and Actinobacteria (6.34%–34.52%) was significantly higher in the permafrost layer than in the active layer, whereas that of Acidobacteria (4.98%–38.82%) exhibited the opposite trend, and the abundance of Proteobacteria (2.49%–22.51%) generally decreased with depth. More importantly, the abundance of bacteria linked to human infectious diseases was significantly higher in the permafrost layer according to Tax4Fun prediction analysis. Redundancy analysis (RDA) showed that ammonium nitrogen (NH4+‐N), total organic carbon (TOC), and total phosphorus (TP) were major factors affecting the bacterial community composition. Collectively, our findings provide insights into the soil bacterial vertical distribution patterns and major environmental drivers in high‐latitude permafrost regions, which is key to grasping the response of cold region ecosystem processes to global climate changes.
Collapse
Affiliation(s)
- Xin Li
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Yuanquan Cui
- Personnel department Harbin Normal University Harbin China
| | - Dalong Ma
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Dandan Song
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Lin Liu
- College of Geographical Sciences Harbin Normal University Harbin China
| |
Collapse
|
11
|
Iqbal A, He L, Ali I, Yuan P, Khan A, Hua Z, Wei S, Jiang L. Partial Substation of Organic Fertilizer With Chemical Fertilizer Improves Soil Biochemical Attributes, Rice Yields, and Restores Bacterial Community Diversity in a Paddy Field. FRONTIERS IN PLANT SCIENCE 2022; 13:895230. [PMID: 35720563 PMCID: PMC9201382 DOI: 10.3389/fpls.2022.895230] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Conventional farming systems are highly reliant on chemical fertilizers (CFs), which adversely affect soil quality, crop production and the environment. One of the major current challenges of current agriculture is finding ways to increase soil health and crop yield sustainably. Manure application as a substitute for CF is an alternative fertilization strategy for maintaining soil health and biodiversity. However, little is known about the complex response of soil bacterial communities and soil nutrients to manure and CFs application. This study reports the response of soil nutrients, rice yield, and soil microbial community structure to 2 years of continuous manure and CFs application. The study consisted of six treatments: no N fertilizer control (Neg-Con); 100% CF (Pos-Con); 60% cattle manure (CM) + 40% CF (High-CM); 30% CM + 70% CF (Low-CM); 60% poultry manure (PM) + 40% CF (High-PM), and 30% PM + 70% CF (Low-PM). We used high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize the soil bacterial communities. Results revealed that the addition of manure significantly altered the soil bacterial community composition and structure; and enhanced the relative abundance of phyla Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Planctomycetes. Organic fertilizer treatments, particularly high CM and PM had the highest measured soil bacterial diversity of all treatments. Similarly, integrated application of manure and CFs increased the soil biochemical traits [i.e., pH, total N (TN), soil organic C (SOC), microbial biomass N (MBN), and microbial biomass C (MBC)] and rice grain yield. Average increases in SOC, TN, MBN, and MBC were 43.66, 31.57, 24.34, and 49.45%, respectively, over the years in the High-PM compared with Pos-Con. Redundancy analysis showed that the dominant bacteria phyla were correlated with soil pH, SOC, TN, and microbial biomass, but the relative abundance of Proteobacteria was strongly correlated with environmental factors such as soil pH, SOC, TN, and MBC. We employed a structural equation model to examine the relationship between microbial biomass, soil nutrients and grain yield among treatments. This analysis supported the hypothesis that soil nutrient content and availability directly affect rice grain yield while soil bacteria indirectly affect grain yield through microbial biomass production and nutrient levels. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.
Collapse
Affiliation(s)
- Anas Iqbal
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Liang He
- College of Agriculture, Guangxi University, Nanning, China
| | - Izhar Ali
- College of Agriculture, Guangxi University, Nanning, China
| | - Pengli Yuan
- College of Agriculture, Guangxi University, Nanning, China
| | - Abdullah Khan
- College of Agriculture, Guangxi University, Nanning, China
| | - Zhang Hua
- College of Agriculture, Guangxi University, Nanning, China
| | - Shanqing Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Ligeng Jiang
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| |
Collapse
|
12
|
Scheel M, Zervas A, Jacobsen CS, Christensen TR. Microbial Community Changes in 26,500-Year-Old Thawing Permafrost. Front Microbiol 2022; 13:787146. [PMID: 35401488 PMCID: PMC8988141 DOI: 10.3389/fmicb.2022.787146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.
Collapse
Affiliation(s)
- Maria Scheel
- Department of Ecoscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | - Torben R. Christensen
- Department of Ecoscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
- Oulanka Research Station, Oulu University, Oulu, Finland
| |
Collapse
|
13
|
Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
Collapse
|
14
|
Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. DIVERSITY 2021. [DOI: 10.3390/d13070328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.
Collapse
|
15
|
Krauze P, Wagner D, Yang S, Spinola D, Kühn P. Influence of prokaryotic microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica. Sci Rep 2021; 11:13135. [PMID: 34162928 PMCID: PMC8222374 DOI: 10.1038/s41598-021-92205-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Compared to the 1970s, the edge of the Ecology Glacier on King George Island, maritime Antarctica, is positioned more than 500 m inwards, exposing a large area of new terrain to soil-forming processes and periglacial climate for more than 40 years. To gain information on the state of soil formation and its interplay with microbial activity, three hyperskeletic Cryosols (vegetation cover of 0-80%) deglaciated after 1979 in the foreland of the Ecology Glacier and a Cambic Cryosol (vegetation cover of 100%) distal to the lateral moraine deglaciated before 1956 were investigated by combining soil chemical and microbiological methods. In the upper part of all soils, a decrease in soil pH was observed, but only the Cambic Cryosol showed a clear direction of pedogenic and weathering processes, such as initial silicate weathering indicated by a decreasing Chemical Index of Alteration with depth. Differences in the development of these initial soils could be related to different microbial community compositions and vegetation coverage, despite the short distance among them. We observed-decreasing with depth-the highest bacterial abundances and microbial diversity at vegetated sites. Multiple clusters of abundant amplicon sequence variants were found depending on the site-specific characteristics as well as a distinct shift in the microbial community structure towards more similar communities at soil depths > 10 cm. In the foreland of the Ecology Glacier, the main soil-forming processes on a decadal timescale are acidification and accumulation of soil organic carbon and nitrogen, accompanied by changes in microbial abundances, microbial community compositions, and plant coverage, whereas quantifiable silicate weathering and the formation of pedogenic oxides occur on a centennial to a millennial timescale after deglaciation.
Collapse
Affiliation(s)
- Patryk Krauze
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany.
| | - Dirk Wagner
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14476, Potsdam, Germany
| | - Sizhong Yang
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Diogo Spinola
- Department of Geosciences, Research Area Geography, Laboratory of Soil Science and Geoecology, Eberhard Karls University Tübingen, 72070, Tübingen, Germany
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, 99775-6160, USA
| | - Peter Kühn
- Department of Geosciences, Research Area Geography, Laboratory of Soil Science and Geoecology, Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| |
Collapse
|
16
|
Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation. Proc Natl Acad Sci U S A 2021; 118:2025321118. [PMID: 34131077 DOI: 10.1073/pnas.2025321118] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Permafrost degradation may induce soil carbon (C) loss, critical for global C cycling, and be mediated by microbes. Despite larger C stored within the active layer of permafrost regions, which are more affected by warming, and the critical roles of Qinghai-Tibet Plateau in C cycling, most previous studies focused on the permafrost layer and in high-latitude areas. We demonstrate in situ that permafrost degradation alters the diversity and potentially decreases the stability of active layer microbial communities. These changes are associated with soil C loss and potentially a positive C feedback. This study provides insights into microbial-mediated mechanisms responsible for C loss within the active layer in degraded permafrost, aiding in the modeling of C emission under future scenarios.
Collapse
|
17
|
Pinel ISM, Hankinson PM, Moed DH, Wyseure LJ, Vrouwenvelder JS, van Loosdrecht MCM. Efficient cooling tower operation at alkaline pH for the control of Legionella pneumophila and other pathogenic genera. WATER RESEARCH 2021; 197:117047. [PMID: 33799081 DOI: 10.1016/j.watres.2021.117047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Efficient control of pathogenic bacteria, specifically Legionella pneumophila, is one of the main concerns when operating industrial cooling towers. Common practices to limit proliferation involves use of disinfectants, leading to formation of disinfection by-product and increase in water corrosiveness. A disinfectant-free Legionella control method would make the industry more environmentally friendly. A pilot-scale cooling tower (1 m3/h) operated with demineralized water was used to investigate the potential of high-pH conditioning as a disinfectant-free alternative for control of L. pneumophila and other pathogens. One control experiment was performed under standard full-scale operation involving sodium hypochlorite dosage. Thereafter 3 alkaline pHs of the cooling water were tested: 9.0, 9.4 and 9.6. The tests lasted between 25 and 35 days. The cooling water from the basins were analysed for total cell count by flow cytometry, L. pneumophila concentration by plate count and occasional qPCR analyses targeting the mip-gene, bacterial and eukaryotic community analyses with 16S and 18S rRNA gene amplicon sequencing, relative abundance of eukaryotic to prokaryotic DNA by qPCR of the 16S and 18S rRNA gene. The L. pneumophila analyses showed considerable growth at pH 9.0 and pH 9.4 but was maintained below detection limit (< 100 CFU/L) at pH 9.6 without disinfection. Interestingly, the results correlated with the overall abundance of protozoa in the water samples but not directly with the relative abundance of specific reported protozoan hosts of Legionella. The pathogenicity based on 16S rRNA gene amplicon sequencing of the cooling water DNA decreased with increasing pH with a strong decline between pH 9.0 and pH 9.4, from 7.1% to 1.6% of relative abundance of pathogenic genera respectively. A strong shift in microbiome was observed between each tested pH and reproducibility of the experiment at pH 9.6 was confirmed with a duplicate test lasting 80 days. High-pH conditioning ≥ 9.6 is therefore considered as an efficient disinfectant-free cooling tower operation for control of pathogenicity, including L. pneumophila.
Collapse
Affiliation(s)
- I S M Pinel
- Delft University of Technology, Faculty of Applied Sciences, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - P M Hankinson
- Evides Industriewater, Schaardijk 150, 3063 NH Rotterdam, the Netherlands
| | - D H Moed
- Evides Industriewater, Schaardijk 150, 3063 NH Rotterdam, the Netherlands
| | - L J Wyseure
- Evides Industriewater, Schaardijk 150, 3063 NH Rotterdam, the Netherlands
| | - J S Vrouwenvelder
- Delft University of Technology, Faculty of Applied Sciences, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands; King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - M C M van Loosdrecht
- Delft University of Technology, Faculty of Applied Sciences, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| |
Collapse
|
18
|
Jin Y, Zhang B, Chen J, Mao W, Lou L, Shen C, Lin Q. Biofertilizer-induced response to cadmium accumulation in Oryza sativa L. grains involving exogenous organic matter and soil bacterial community structure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 211:111952. [PMID: 33513523 DOI: 10.1016/j.ecoenv.2021.111952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
The accumulation of cadmium (Cd) in Oryza sativa L., the world's most significant staple crop, is a health threat to millions of people. The objective of this study was to evaluate the effectiveness of commercially available biofertilizers (with high (BF2) and low organic matter (OM) content (BF1)) on Cd accumulation in two types of soils and to determine the bacterial community responses by high-throughput sequencing. The study was conducted in the form of pot experiment in greenhouse in 2018. Four treatments were set: BF1, BF2, organic fertilizer (OF), and control (CK) and the amendments were applied before the rice cultivation. The results showed that the addition of biofertilizers immobilized or mobilized Cd in soils, depending on the soil type and the OM content in biofertilizers. The exogenous OM in biofertilizers was the driving factor for the difference in pH and Cd accumulation in rice grains. The application of biofertilizers with high OM content was effective in reducing Cd accumulation in the rice grains (19.7% lower than CK) by significantly increasing soil pH (from 6.02 to 6.67) in acid silt loam soil (TZ). The consumption of acid fermentation products by soil chemoorganotrophs and the complexation of organic anions in the biofertilizer treatment tended to buffer the pH drop in the drainage and decrease the Cd availability. However, in the weak acid silty clay loam soil (SX), the addition of biofertilizer with high OM significantly increased Cd accumulation in rice grains (21.9% higher than CK), probably owing to the release of acid substances, resulting from the significant increase of the predominant bacteria Chloroflexi. The addition of biofertilizer with low OM content did not significantly change Cd accumulation in rice grains or affect the soil microbial structures in both soils. In conclusion, the effects of biofertilizer on rice Cd accumulation were related to the OM content and soil bacterial community. Biofertilizers with high organic matter may not be suitable for amendments in the paddy soils with high clay content to reduce Cd accumulation in rice grains.
Collapse
Affiliation(s)
- Yu Jin
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China
| | - Baofeng Zhang
- Hangzhou Environmental Monitoring Central Station, 310007 Hangzhou, China
| | - Junqiao Chen
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China
| | - Weihua Mao
- The Center of Analysis and Measurement, Zhejiang University, Hangzhou 310058, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China
| | - Qi Lin
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China.
| |
Collapse
|
19
|
Canini F, Zucconi L, Coleine C, D'Alò F, Onofri S, Geml J. Expansion of shrubs could result in local loss of soil bacterial richness in Western Greenland. FEMS Microbiol Ecol 2021; 96:5865694. [PMID: 32609325 DOI: 10.1093/femsec/fiaa089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/08/2020] [Indexed: 12/28/2022] Open
Abstract
Climate warming in Greenland is facilitating the expansion of shrubs across wide areas of tundra. Given the close association between plants and soil microorganisms and the important role of soil bacteria in ecosystem functioning, it is of utmost importance to characterize microbial communities of arctic soil habitats and assess the influence of plant edaphic factors on their composition. We used 16S rRNA gene amplicons to explore the bacterial assemblages of three different soil habitats representative of a plant coverage gradient: bare ground, biological soil crusts dominated by mosses and lichens and vascular vegetation dominated by shrubs. We investigated how bacterial richness and community composition were affected by the vegetation coverage, and soil pH, moisture and carbon (C), nitrogen (N) and phosphorus (P) contents. Bacterial richness did not correlate with plant coverage complexity, while community structure varied between habitats. Edaphic variables affected both the taxonomic richness and community composition. The high number of Amplicon Sequence Variants (ASVs) indicators of bare ground plots suggests a risk of local bacterial diversity loss due to expansion of vascular vegetation.
Collapse
Affiliation(s)
- Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - József Geml
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Leiden, The Netherlands.,MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Eger, Hungary
| |
Collapse
|
20
|
Sajjad W, Ali B, Bahadur A, Ghimire PS, Kang S. Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China. MICROBIAL ECOLOGY 2021; 81:370-384. [PMID: 32918153 DOI: 10.1007/s00248-020-01600-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.
Collapse
Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
| |
Collapse
|
21
|
Zhao X, Huang J, Zhu X, Chai J, Ji X. Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17165680. [PMID: 32781566 PMCID: PMC7460318 DOI: 10.3390/ijerph17165680] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 01/24/2023]
Abstract
The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun'an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun'an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (PN). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.
Collapse
Affiliation(s)
- Xingqing Zhao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China; (J.H.); (X.Z.)
- Correspondence: (X.Z.); (X.J.)
| | - Jian Huang
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China; (J.H.); (X.Z.)
| | - Xuyan Zhu
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China; (J.H.); (X.Z.)
| | - Jinchun Chai
- Department of Civil Engineering and Architecture, Saga University, Saga 8408502, Japan;
| | - Xiaoli Ji
- School of Economics, Changzhou University, Changzhou 213164, China
- Correspondence: (X.Z.); (X.J.)
| |
Collapse
|
22
|
Solanki MK, Wang Z, Wang FY, Li CN, Gupta CL, Singh RK, Malviya MK, Singh P, Yang LT, Li YR. Assessment of Diazotrophic Proteobacteria in Sugarcane Rhizosphere When Intercropped With Legumes (Peanut and Soybean) in the Field. Front Microbiol 2020; 11:1814. [PMID: 32849421 PMCID: PMC7412970 DOI: 10.3389/fmicb.2020.01814] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/10/2020] [Indexed: 12/20/2022] Open
Abstract
Several factors influenced the sugarcane production, and among them, higher use of nitrogen and depletion of soil nutrient constitutes a significant concern in China. Sugarcane-legume intercropping may help to regulate the microbial structure and functions. In the present study, sugarcane rhizosphere soils of three cropping systems: Sugarcane only (S-only), sugarcane with peanut (S + P), and sugarcane + soybean (S + S) were sampled in tillering, elongation, and maturation stages from two different experimental fields. High-throughput sequencing technologies applied to assess the effects of different cropping systems on the structure of nitrogenase (nifH) gene communities. A total of 3818 OTUs (operational taxonomic units) were acquired from all soil samples. Intercropping systems noticeably increased the relative abundance of Proteobacteria in the tillering stage. The increased microbial diversity in the rhizosphere was mainly due to soil organic carbon and total soil N. In contrast, intercropping has no significant negative impact on microbial abundance, but sugarcane growth stages influence it significantly, and two bacteria (Bradyrhizobium and Pseudacidovorax) showed significant shift during plant growth. The results provide insight into the microbial structure of Proteobacteria in the sugarcane legume-intercropping field, and how microbial community behaves in different growth stages. It can boost the microbial activity of the soil, and that could be a new strategy to stimulate soil fertility without causing any negative impact on crop production.
Collapse
Affiliation(s)
- Manoj Kumar Solanki
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Zhen Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Fei-Yong Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chang-Ning Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chhedi Lal Gupta
- The Volcani Center, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Rajesh Kumar Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh Kumar Malviya
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Pratiksha Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Yang-Rui Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| |
Collapse
|
23
|
Zhang L, Zhong M, Li X, Lu W, Li J. River bacterial community structure and co-occurrence patterns under the influence of different domestic sewage types. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 266:110590. [PMID: 32310123 DOI: 10.1016/j.jenvman.2020.110590] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Bacterial communities play a critical role in food webs and the biogeochemical cycles of fundamental elements. However, there remains a substantial gap in our knowledge of the anthropogenic impacts on bacterial co-occurrence patterns and ecosystem functions. In this study, we used Illumina high-throughput sequencing to characterize and compare the diversity, composition, co-occurrence patterns, and functional changes in bacterial communities in the Qingliu River under the influence of different types of domestic sewage. Twelve samples had similar dominant phyla, mainly Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, differing only in the proportions of the microorganisms. However, there was a large difference at the genus level, for example, the relative abundance of the genus Dechloromonas in the school sewage water samples (XXW) was much higher than that in the other samples, the genus Chryseobacterium was the dominant bacteria in the residential sewage water samples (JMW), and there were significant differences between the different samples (P < 0.01). This may indicate that external pollution and environmental induction deeply affect the bacterial community assembly in rivers. Network analysis showed that the river bacterial co-occurrence network has a modular structure (divided into 6 modules), and that the microbial taxonomic units from the same module were involved in the carbon and nitrogen cycle (e.g., the CL500-29 marine group and the genus Pseudomonas) and degradation of organic pollutants and toxic compounds (e.g., the genera Massilia and Exiguobacterium). Functional predictions indicate that the function of ABC transporter was highest in the hospital sewage water samples (YYW), while two-component system was more abundant in the XXW samples. In summary, our research provides a new perspective of community assembly in rivers under the influence of human activity.
Collapse
Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Mengmeng Zhong
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| |
Collapse
|
24
|
Malard LA, Anwar MZ, Jacobsen CS, Pearce DA. Biogeographical patterns in soil bacterial communities across the Arctic region. FEMS Microbiol Ecol 2020; 95:5552140. [PMID: 31429869 PMCID: PMC6736398 DOI: 10.1093/femsec/fiz128] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 11/14/2022] Open
Abstract
The considerable microbial diversity of soils and key role in biogeochemical cycling have led to growing interest in their global distribution and the impact that environmental change might have at the regional level. In the broadest study of Arctic soil bacterial communities to date, we used high-throughput DNA sequencing to investigate the bacterial diversity from 200 independent Arctic soil samples from 43 sites. We quantified the impact of spatial and environmental factors on bacterial community structure using variation partitioning analysis, illustrating a nonrandom distribution across the region. pH was confirmed as the key environmental driver structuring Arctic soil bacterial communities, while total organic carbon (TOC), moisture and conductivity were shown to have little effect. Specialist taxa were more abundant in acidic and alkaline soils while generalist taxa were more abundant in acidoneutral soils. Of the 48 147 bacterial taxa, a core microbiome composed of only 13 taxa that were ubiquitously distributed and present within 95% of samples was identified, illustrating the high potential for endemism in the region. Overall, our results demonstrate the importance of spatial and edaphic factors on the structure of Arctic soil bacterial communities.
Collapse
Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK
| | - Muhammad Z Anwar
- Department of Environmental Sciences, Aarhus University, 4000 Roskilde, Denmark
| | - Carsten S Jacobsen
- Department of Environmental Sciences, Aarhus University, 4000 Roskilde, Denmark
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK.,British Antarctic Survey, High Cross Madingley Road, Cambridge CB3 0ET, United Kingdom
| |
Collapse
|
25
|
Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
|
26
|
Zhang L, Cheng Y, Gao G, Jiang J. Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16203966. [PMID: 31627458 PMCID: PMC6844080 DOI: 10.3390/ijerph16203966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022]
Abstract
Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.
Collapse
Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China.
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Yu Cheng
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China.
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Jiahu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| |
Collapse
|
27
|
Ali B, Sajjad W, Ghimire PS, Shengyun C, Minghui W, Kang S. Culture-dependent diversity of bacteria from Laohugou glacier, Qilian Mts., China and their resistance against metals. J Basic Microbiol 2019; 59:1065-1081. [PMID: 31556143 DOI: 10.1002/jobm.201900385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/23/2019] [Accepted: 09/07/2019] [Indexed: 11/08/2022]
Abstract
In the current study, psychrophilic, endolithic, and epilithic bacterial strains were isolated and characterized from the nonpolar Laohugou glacier (LHG) no. 12, the largest valley glacier in the western Qilian Mts. located on the northeastern edge of the Tibetan Plateau. Five different types of samples, rocks, soil, glacial water, ice/snow, and cryoconite, were collected. A total of 48 bacterial strains were isolated by using the R2A bacterial cultural medium. The findings revealed that the Gram-positive bacteria 41 (85.4%) dominated the Gram-negative bacteria 7 (14.6%) in this extremely harsh environment. Molecular characterization based on 16S ribosomal RNA gene sequencing exhibited that the obtained isolates belong to four phyla, among which the diversity of Firmicutes (58.33%) was higher followed by Actinobacteria (23.0%), Proteobacteria (14.6%), and least diversity was reported in Euryarchaeota (4.2%). The bacterial communities were most dominant in soil samples followed by cryoconite sample and least dominant in the ice and snow samples. Moreover, the obtained bacterial isolates were found resistant to high concentrations of heavy metals (Cr3+ , Cd2+ , Hg2+ , and Ar3+ ) and sodium chloride, and, therefore, exhibited polyextremophilic characteristics. LHG no. 12 is rich in bacterial and archaeal diversities and provides a potentially curious site for further in-depth exploration of microbial diversity and their biotechnological applications.
Collapse
Affiliation(s)
- Barkat Ali
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wasim Sajjad
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Prakriti Sharma Ghimire
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China.,Himalayan Environment Research Institute (HERI), Kathmandu, Nepal
| | - Chen Shengyun
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China
| | - Wu Minghui
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China
| | - Shichang Kang
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
| |
Collapse
|
28
|
Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
Collapse
Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
| |
Collapse
|
29
|
Malard LA, Šabacká M, Magiopoulos I, Mowlem M, Hodson A, Tranter M, Siegert MJ, Pearce DA. Spatial Variability of Antarctic Surface Snow Bacterial Communities. Front Microbiol 2019; 10:461. [PMID: 30972032 PMCID: PMC6443967 DOI: 10.3389/fmicb.2019.00461] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
It was once a long-held view that the Antarctic was a pristine environment with low biomass, low biodiversity and low rates of microbial activity. However, as the intensity of scientific investigation has increased, so these views have started to change. In particular, the role and impact of human activity toward indigenous microbial communities has started to come under more intense scrutiny. During the Subglacial Lake Ellsworth exploration campaign in December 2012, a microbiological survey was conducted to determine the extent and likelihood of exogenous input into the subglacial lake system during the hot-water drilling process. Snow was collected from the surface to represent that used for melt water production for hot-water drilling. The results of this study showed that snow used to provide melt water differed in its microbiological composition from that of the surrounding area and raised the question of how the biogeography of snow-borne microorganisms might influence the potential outcome of scientific analyses. In this study, we investigated the biogeography of microorganisms in snow around a series of Antarctic logistic hubs, where human activity was clearly apparent, and from which scientific investigations have been undertaken. A change in microbial community structure with geographical location was apparent and, notably, a decrease in alpha diversity at more remote southern latitudes. Soil-related microorganisms dominated microbial assemblages suggesting terrestrial input, most likely from long-range aeolian transport into continental Antarctica. We also observed that relic DNA was not a major issue when assessing snow samples. Overall, our observations might have profound implications for future scientific activities in Antarctica, such as the need to establish "no-go" protected areas, the need for better characterization of field sites and improved protocols for sterilization and verification of ice drilling equipment.
Collapse
Affiliation(s)
- Lucie A. Malard
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle upon Tyne, United Kingdom
| | - Marie Šabacká
- Centre for Polar Ecology, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Iordanis Magiopoulos
- Institute of Oceanography, Hellenic Centre for Marine Research, Heraklion, Greece
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, United Kingdom
| | - Matt Mowlem
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, United Kingdom
| | - Andy Hodson
- Arctic Geology, University Centre in Svalbard, Longyearbyen, Norway
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Martyn Tranter
- Bristol Glaciology Centre, University of Bristol, Bristol, United Kingdom
| | - Martin J. Siegert
- Grantham Institute, Department of Earth Science and Engineering, Imperial College London, London, United Kingdom
| | - David A. Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle upon Tyne, United Kingdom
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| |
Collapse
|
30
|
Malard LA, Pearce DA. Microbial diversity and biogeography in Arctic soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:611-625. [PMID: 30028082 DOI: 10.1111/1758-2229.12680] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO2 , CH4 and N2 O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.
Collapse
Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| |
Collapse
|
31
|
de Jong AEE, In 't Zandt MH, Meisel OH, Jetten MSM, Dean JF, Rasigraf O, Welte CU. Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments. Environ Microbiol 2018; 20:4314-4327. [PMID: 29968310 PMCID: PMC6334529 DOI: 10.1111/1462-2920.14345] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 11/30/2022]
Abstract
Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH4) and carbon dioxide (CO2). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH4production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.
Collapse
Affiliation(s)
- Anniek E E de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Ove H Meisel
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Joshua F Dean
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
32
|
Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE. Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources. Front Microbiol 2018; 9:1192. [PMID: 29930542 PMCID: PMC6000721 DOI: 10.3389/fmicb.2018.01192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/16/2018] [Indexed: 12/04/2022] Open
Abstract
Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.
Collapse
Affiliation(s)
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kevin P Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| |
Collapse
|
33
|
Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep 2018; 8:504. [PMID: 29323168 PMCID: PMC5765012 DOI: 10.1038/s41598-017-18777-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.
Collapse
|
34
|
Chen YL, Deng Y, Ding JZ, Hu HW, Xu TL, Li F, Yang GB, Yang YH. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Mol Ecol 2017; 26:6608-6620. [DOI: 10.1111/mec.14396] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 09/29/2017] [Accepted: 10/13/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Yong-Liang Chen
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Jin-Zhi Ding
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Tian-Le Xu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Gui-Biao Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Yuan-He Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| |
Collapse
|
35
|
Singh P, Singh SM, Singh RN, Naik S, Roy U, Srivastava A, Bölter M. Bacterial communities in ancient permafrost profiles of Svalbard, Arctic. J Basic Microbiol 2017; 57:1018-1036. [DOI: 10.1002/jobm.201700061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/13/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Purnima Singh
- Birla Institute of Technology and Science (BITS); Pilani-K.K. Birla Goa Campus; Zuarinagar Goa India
| | - Shiv M. Singh
- National Centre for Antarctic and Ocean Research; Ministry of Earth Sciences; Vasco-Da-Gama Goa India
| | - Ram N. Singh
- National Bureau of Agriculturally Important Microorganisms (NBAIM); Uttar Pradesh India
| | - Simantini Naik
- National Centre for Antarctic and Ocean Research; Ministry of Earth Sciences; Vasco-Da-Gama Goa India
| | - Utpal Roy
- Birla Institute of Technology and Science (BITS); Pilani-K.K. Birla Goa Campus; Zuarinagar Goa India
| | - Alok Srivastava
- National Bureau of Agriculturally Important Microorganisms (NBAIM); Uttar Pradesh India
| | - Manfred Bölter
- Institute of Ecosystem Research; Christian-Albrechts-Universität zu Kiel; Kiel Germany
| |
Collapse
|
36
|
Shcherbakova V, Yoshimura Y, Ryzhmanova Y, Taguchi Y, Segawa T, Oshurkova V, Rivkina E. Archaeal communities of Arctic methane-containing permafrost. FEMS Microbiol Ecol 2016; 92:fiw135. [DOI: 10.1093/femsec/fiw135] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/06/2023] Open
|
37
|
Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol 2016; 92:fiw018. [DOI: 10.1093/femsec/fiw018] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 01/08/2023] Open
|
38
|
Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting. Metabolites 2016; 6:metabo6010002. [PMID: 26761036 PMCID: PMC4812331 DOI: 10.3390/metabo6010002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/23/2015] [Accepted: 12/30/2015] [Indexed: 01/02/2023] Open
Abstract
The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149–2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations.
Collapse
|
39
|
Arctic soil microbial diversity in a changing world. Res Microbiol 2015; 166:796-813. [DOI: 10.1016/j.resmic.2015.07.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/23/2023]
|
40
|
Pushkareva E, Pessi IS, Wilmotte A, Elster J. Cyanobacterial community composition in Arctic soil crusts at different stages of development. FEMS Microbiol Ecol 2015; 91:fiv143. [PMID: 26564957 PMCID: PMC4668365 DOI: 10.1093/femsec/fiv143] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
Cyanobacterial diversity in soil crusts has been extensively studied in arid lands of temperate regions, particularly semi-arid steppes and warm deserts. Nevertheless, Arctic soil crusts have received far less attention than their temperate counterparts. Here, we describe the cyanobacterial communities from various types of soil crusts from Svalbard, High Arctic. Four soil crusts at different development stages (ranging from poorly-developed to well-developed soil crusts) were analysed using 454 pyrosequencing of the V3-V4 variable region of the cyanobacterial 16S rRNA gene. Analyses of 95 660 cyanobacterial sequences revealed a dominance of OTUs belonging to the orders Synechococcales, Oscillatoriales and Nostocales. The most dominant OTUs in the four studied sites were related to the filamentous cyanobacteria Leptolyngbya sp. Phylotype richness estimates increased from poorly- to mid-developed soil crusts and decreased in the well-developed lichenized soil crust. Moreover, pH, ammonium and organic carbon concentrations appeared significantly correlated with the cyanobacterial community structure.
Collapse
Affiliation(s)
- Ekaterina Pushkareva
- Centre for Polar Ecology, University of South Bohemia, 37005 ČeskéBudějovice, Czech Republic
| | - Igor S Pessi
- Centre for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, 37005 ČeskéBudějovice, Czech Republic Institute of Botany, Academy of Science of the Czech Republic, 37982 Třeboň, Czech Republic
| |
Collapse
|
41
|
Hill R, Saetnan ER, Scullion J, Gwynn-Jones D, Ostle N, Edwards A. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure. Environ Microbiol 2015; 18:1942-53. [DOI: 10.1111/1462-2920.13017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Richard Hill
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| | - Eli R. Saetnan
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - John Scullion
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Dylan Gwynn-Jones
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Nick Ostle
- Plant and Soil Ecology Laboratory; Lancaster Environmental Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| |
Collapse
|
42
|
Coolen MJL, Orsi WD. The transcriptional response of microbial communities in thawing Alaskan permafrost soils. Front Microbiol 2015; 6:197. [PMID: 25852660 PMCID: PMC4360760 DOI: 10.3389/fmicb.2015.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.
Collapse
Affiliation(s)
- Marco J. L. Coolen
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
- Western Australia Organic and Isotope Geochemistry Centre, Department of Chemistry, Curtin UniversityPerth, WA, Australia
| | - William D. Orsi
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
| |
Collapse
|
43
|
Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Čapek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol 2014; 5:541. [PMID: 25360132 PMCID: PMC4199454 DOI: 10.3389/fmicb.2014.00541] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/29/2014] [Indexed: 01/04/2023] Open
Abstract
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.
Collapse
Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Department of Bioscience, Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Jörg Schnecker
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Birgit Wild
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Petr Čapek
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Vigdis L. Torsvik
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| |
Collapse
|