1
|
Madariaga-Troncoso D, Vargas I, Rojas-Villalta D, Abanto M, Núñez-Montero K. Metataxonomics Characterization of Soil Microbiome Extraction Method Using Different Dispersant Solutions. Microorganisms 2025; 13:936. [PMID: 40284772 PMCID: PMC12029719 DOI: 10.3390/microorganisms13040936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/07/2025] [Accepted: 04/15/2025] [Indexed: 04/29/2025] Open
Abstract
Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed soils; however, direct soil transfer presents practical limitations for large-scale applications. An alternative strategy involves extracting microbial communities through soil washing processes, but its success highly depends on proper microbiota characterization and efficient extraction methods. This study evaluated a soil wash method using four different dispersant solutions (Tween-80, NaCl, sodium citrate, and sodium pyrophosphate) for their ability to extract the majority of microbial cells from Antarctic and Crop soils. The extracted microbiomes were analyzed using 16S rRNA gene metataxonomics to assess their diversity and abundance. We found that some treatments extracted a greater proportion of specific taxa, and, on the other hand, some extracted a lower proportion than the control treatment. In addition, these dispersant solutions showed the extraction of the relevant microbial community profile in soil samples, composed of multiple taxa, including beneficial bacteria for soil health. Our study aims to optimize DNA extraction methods for microbiome analyses and to explore the use of this technique in various biotechnological applications. The results provide insights into the effect of dispersant solutions on microbiome extractions. In this regard, sodium chloride could be optimal for Antarctic soils, while sodium citrate is suggested for the Crop soils.
Collapse
Affiliation(s)
- David Madariaga-Troncoso
- Facultad de Ciencias de La Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Isaac Vargas
- Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica;
| | - Dorian Rojas-Villalta
- Cellular and Molecular Biology Research Center, Universidad de Costa Rica, San José 11501, Costa Rica;
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar, Temuco 4811230, Chile
| | - Kattia Núñez-Montero
- Facultad de Ciencias de La Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| |
Collapse
|
2
|
Geng P, Ma A, Wei X, Chen X, Yin J, Hu F, Zhuang X, Song M, Zhuang G. Interaction and spatio-taxonomic patterns of the soil microbiome around oil production wells impacted by petroleum hydrocarbons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119531. [PMID: 35623572 DOI: 10.1016/j.envpol.2022.119531] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Numerous onshore oil production wells currently exist, and the petroleum hydrocarbon contamination of the surrounding soil caused by oil production wells is not well understood. Moreover, the impact of the distribution of the total petroleum hydrocarbons (TPH) in the soil on the microbiota requires further investigation. Accordingly, in this study, the distribution of petroleum hydrocarbons in the soils around oil production wells was investigated, and their alteration of the microbiota was revealed. The results revealed that in the horizontal direction, the heavily TPH-contaminated soils were mainly distributed within a circle with a radius of 200 cm centered on the oil production well; and in the vertical direction, the heavily TPH-contaminated soils were distributed within the 0-50 cm soil layer. A significant positive correlation was found between the microbial abundance and the TPH concentration in the soil with relatively low total carbon contents. Heavy TPH contamination (TPH concentration of >3000 mg/kg) significantly reduced the microbial diversity and altered the microbiota compared with the light TPH contamination (TPH concentration of around 1000 mg/kg). In the heavily TPH-contaminated soils, the relative abundances of the Proteobacteria and Bacteroides increased significantly; the network complexity among the soil microorganisms decreased; and the co-occurrence patterns were altered. In summary, the results of this study have reference value in the remediation of soils around oil production wells and provide guidance for the construction of microbial remediation systems for petroleum contamination.
Collapse
Affiliation(s)
- Pengxue Geng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anzhou Ma
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaoxia Wei
- Drilling and Production Technology Research Institute, PetroChina Qinghai Oil Field, Dunhuang, 736202, China
| | - Xianke Chen
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Jun Yin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Futang Hu
- Drilling and Production Technology Research Institute, PetroChina Qinghai Oil Field, Dunhuang, 736202, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Maoyong Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
3
|
Dong X, Liu C, Ma D, Wu Y, Man H, Wu X, Li M, Zang S. Organic Carbon Mineralization and Bacterial Community of Active Layer Soils Response to Short-Term Warming in the Great Hing'an Mountains of Northeast China. Front Microbiol 2022; 12:802213. [PMID: 35003032 PMCID: PMC8739994 DOI: 10.3389/fmicb.2021.802213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
As a buffer layer for the energy and water exchange between atmosphere and permafrost, the active layer is sensitive to climate warming. Changes in the thermal state in active layer can alter soil organic carbon (SOC) dynamics. It is critical to identify the response of soil microbial communities to warming to better predict the regional carbon cycle under the background of global warming. Here, the active layer soils collected from a wetland-forest ecotone in the continuous permafrost region of Northeastern China were incubated at 5 and 15°C for 45 days. High-throughput sequencing of the 16S rRNA gene was used to examine the response of bacterial community structure to experimental warming. A total of 4148 OTUs were identified, which followed the order 15°C > 5°C > pre-incubated. Incubation temperature, soil layer and their interaction have significant effects on bacterial alpha diversity (Chao index). Bacterial communities under different temperature were clearly distinguished. Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria accounted for more than 80% of the community abundance at the phylum level. Warming decreased the relative abundance of Chloroflexi and Acidobacteria, while Actinobacteria and Proteobacteria exhibited increasing trend. At family level, the abundance of norank_o__norank_c__AD3 and Ktedonobacteraceae decreased significantly with the increase of temperature, while Micrococcaccac increased. In addition, the amount of SOC mineralization were positively correlated with the relative abundances of most bacterial phyla and SOC content. SOC content was positively correlated with the relative abundance of most bacterial phyla. Results indicate that the SOC content was the primary explanatory variable and driver of microbial regulation for SOC mineralization. Our results provide a new perspective for understanding the microbial mechanisms that accelerates SOC decomposition under warming conditions in the forest-wetland ecotone of permafrost region.
Collapse
Affiliation(s)
- Xingfeng Dong
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Chao Liu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Dalong Ma
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Yufei Wu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Haoran Man
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Xiangwen Wu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Miao Li
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Shuying Zang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| |
Collapse
|
4
|
Lifshits S, Glyaznetsova Y, Erofeevskaya L, Chalaya O, Zueva I. Effect of oil pollution on the ecological condition of soils and bottom sediments of the arctic region (Yakutia). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 288:117680. [PMID: 34284204 DOI: 10.1016/j.envpol.2021.117680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/06/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Oil and petroleum products are known to be among the most widespread soil pollutants. The risk of emergencies is sure to increase greatly in conditions of abnormally low temperatures. Oil and oil products are not only toxic to the environment, but can also have a negative impact on the state of the permafrost zone, accelerating the processes of permafrost degradation. The goal of the research was to study the soils and bottom sediments for oil pollution in the Arctic region of Yakutia. The research was carried out with using the complex of geochemical and microbiological methods of analysis. It had shown that at present oil pollution was mainly concentrated on the objects bearing a high technogenic load. However, some migration of hydrocarbons was observed with melt, seasonal melt and rainwaters, as a result of which the natural background of the nearby territories became technogenic character. In the Arctic conditions for the first time according to the obtained data on geochemical and microbiological studies oxidative destruction of oil pollutants in soil occurred mainly under the influence of physic and chemical environmental factors, not by microbial oxidation. Sluggish processes of mineralization of organic residues and the transformation of oil pollutants by the type of putrefaction led to the colonization of oil-polluted soils of the Arctic with putrefying and pathogenic microorganisms. The purpose of further research will be studying the possibility of intensification of soil remediation processes of technologically disturbed soils at abnormally low temperatures.
Collapse
Affiliation(s)
- Sara Lifshits
- Institute of Oil and Gas Problems of Federal Research Center "Yakut Scientific Center of Siberian Branch of the Russian Academy of Sciences", 677980, Petrovsky St., 2, Yakutsk, Russia.
| | - Yuliya Glyaznetsova
- Institute of Oil and Gas Problems of Federal Research Center "Yakut Scientific Center of Siberian Branch of the Russian Academy of Sciences", 677980, Petrovsky St., 2, Yakutsk, Russia
| | - Larisa Erofeevskaya
- Institute of Oil and Gas Problems of Federal Research Center "Yakut Scientific Center of Siberian Branch of the Russian Academy of Sciences", 677980, Petrovsky St., 2, Yakutsk, Russia
| | - Olga Chalaya
- Institute of Oil and Gas Problems of Federal Research Center "Yakut Scientific Center of Siberian Branch of the Russian Academy of Sciences", 677980, Petrovsky St., 2, Yakutsk, Russia
| | - Iraida Zueva
- Institute of Oil and Gas Problems of Federal Research Center "Yakut Scientific Center of Siberian Branch of the Russian Academy of Sciences", 677980, Petrovsky St., 2, Yakutsk, Russia
| |
Collapse
|
5
|
Wong RR, Lim ZS, Shaharuddin NA, Zulkharnain A, Gomez-Fuentes C, Ahmad SA. Diesel in Antarctica and a Bibliometric Study on Its Indigenous Microorganisms as Remediation Agent. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041512. [PMID: 33562609 PMCID: PMC7915771 DOI: 10.3390/ijerph18041512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminants in their natural state are known to be persistent, complex and toxic. The low temperature in Antarctica worsens these issues, making pollutants more significantly toxic to their environment and indigenous organisms. A bibliometric analysis had demonstrated a gradual increase in the number of studies on the microbial hydrocarbon remediation in Antarctica over the year. It was also found that these studies were dominated by those that used bacteria as remediating agents, whereas very little focus was given on fungi and microalgae. This review presents a summary of the collective and past understanding to the current findings of Antarctic microbial enzymatic degradation of hydrocarbons as well as its genotypic adaptation to the extreme low temperature.
Collapse
Affiliation(s)
- Rasidnie Razin Wong
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Zheng Syuen Lim
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, College of Systems Engineering and Science, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
- National Antarctic Research Centre, Universiti Malaya B303 Level 3, Block B, IPS Building, Kuala Lumpur 50603, Malaysia
- Correspondence:
| |
Collapse
|
6
|
Figueroa-Gonzalez PA, Bornemann TLV, Adam PS, Plewka J, Révész F, von Hagen CA, Táncsics A, Probst AJ. Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. Front Microbiol 2020; 11:587782. [PMID: 33424787 PMCID: PMC7786006 DOI: 10.3389/fmicb.2020.587782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/03/2020] [Indexed: 01/05/2023] Open
Abstract
Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.
Collapse
Affiliation(s)
- Perla Abigail Figueroa-Gonzalez
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Julia Plewka
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Fruzsina Révész
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Christian A von Hagen
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Alexander J Probst
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
7
|
Li A, Li G, Yang J, Yang Y, Liang Y, Zhang D. Geo-distribution pattern of microbial carbon cycling genes responsive to petroleum contamination in continental horizontal oilfields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139188. [PMID: 32402908 DOI: 10.1016/j.scitotenv.2020.139188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Contamination significantly affects soil microbial community structures, and the metabolisms of organic contaminants might particularly alter soil carbon cycling by shaping microbial carbon cycling genes. Although numerous studies have discussed the impacts of petroleum contamination on soil bacterial communities and relevant degrading genes, there is no work addressing how soil carbon cycling genes are affected by petroleum contamination. In this study, 77 soil samples were collected from five typical oilfields horizontally located in China to explore the influence of environmental variables and petroleum contamination on microbial carbon cycling genes. Results from Geochip suggested a geographic-determined distribution of carbon cycling genes. Although no significant correlation was observed between carbon cycling genes and soil physio-chemical properties for all soils, some relationships were identified in specific oilfield. Principle component analysis indicated that soil physio-chemical properties, rather than petroleum contamination disturbance, are the key factors determining the degree of sample dispersion, whereas environmental variables predominantly control the degree of sample aggregation. Co-occurrence ecological network analysis revealed a more complex interactions of all functional genes in petroleum-contaminated soils, and carbon cycling genes were grouped with nitrogen related genes in petroleum-contaminated communities. Soil moisture and heterogeneity were identified as the main drivers for the abundance and diversity of carbon cycling genes, particularly in petroleum-contaminated soils. These results are attributing to the fewer impacts of petroleum contamination on the diversity of carbon cycling genes than soil physio-chemical properties, and soil carbon cycling genes are mainly driven by geographic location and petroleum contamination together. Our findings provide deeper insight into the influence of petroleum contamination in soil microbial functions related to carbon cycling.
Collapse
Affiliation(s)
- Aiyang Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China
| | - Juejie Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China.
| |
Collapse
|
8
|
Gaete A, Mandakovic D, González M. Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics. Microorganisms 2020; 8:microorganisms8081213. [PMID: 32785053 PMCID: PMC7466141 DOI: 10.3390/microorganisms8081213] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/15/2022] Open
Abstract
The isolation of soil bacteria from extreme environments represents a major challenge, but also an opportunity to characterize the metabolic potential of soil bacteria that could promote the growth of plants inhabiting these harsh conditions. The aim of this study was to isolate and identify bacteria from two Chilean desert environments and characterize the beneficial traits for plants through a biochemical approach. By means of different culture strategies, we obtained 39 bacterial soil isolates from the Coppermine Peninsula (Antarctica) and 32 from Lejía Lake shore soil (Atacama Desert). The results obtained from the taxonomic classification and phylogenetic analysis based on 16S rDNA sequences indicated that the isolates belonged to four phyla (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes), and that the most represented genus at both sites was Pseudomonas. Regarding biochemical characterization, all strains displayed in vitro PGP capabilities, but these were in different proportions that grouped them according to their site of origin. This study contributes with microbial isolates from natural extreme environments with biotechnological potentials in improving plant growth under cold stress.
Collapse
Affiliation(s)
- Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile. Santa Rosa 11315, 8820808 Santiago, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Camino La Pirámide 5750, 8320000 Santiago, Chile;
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LGIB). Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile. El Líbano 5524, 7810000 Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Correspondence:
| |
Collapse
|
9
|
Newsham KK, Tripathi BM, Dong K, Yamamoto N, Adams JM, Hopkins DW. Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil. MICROBIAL ECOLOGY 2019; 78:974-984. [PMID: 30989354 DOI: 10.1007/s00248-019-01373-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.
Collapse
Affiliation(s)
- Kevin K Newsham
- NERC British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Binu M Tripathi
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ke Dong
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-do, 16227, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jonathan M Adams
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - David W Hopkins
- Scotland's Rural College, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| |
Collapse
|
10
|
Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
Collapse
Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| |
Collapse
|
11
|
Karačić S, Wilén BM, Suarez C, Hagelia P, Persson F. Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities. BIOFOULING 2018; 34:1161-1174. [PMID: 30740996 DOI: 10.1080/08927014.2018.1556259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Deterioration of concrete is a large societal cost. In the Oslofjord subsea tunnel (Norway), deterioration of sprayed concrete and corrosion of reinforcing steel fibres occur under biofilm formed at sites with intrusion of saline groundwater. In this study, the microbial community structure, in situ environmental gradients and chemical composition of the biofilms were examined at three tunnel sites. Ammonia- and nitrite-oxidising microorganisms, in particular Nitrosopumilus sp., and iron-oxidising bacteria within Mariprofundus sp., were omnipresent, together with a diversity of presumably heterotrophic bacteria. Alpha- and beta diversity measures showed significant differences in richness and community structure between the sites as well as over time and null-models suggested that deterministic factors were important for the community assembly. The superficial flow of water over the biofilm had a strong effect on oxygen penetration in the biofilm and was identified as one major environmental gradient that varied between the sites, likely being important for shaping the microbial communities.
Collapse
Affiliation(s)
- Sabina Karačić
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Carolina Suarez
- b Department of Chemistry and Molecular Biology , University of Gothenburg , Göteborg , Göteborg , Sweden
| | - Per Hagelia
- c Tunnel and Concrete Division , The Norwegian Public Roads Administration , Oslo , Norway
| | - Frank Persson
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| |
Collapse
|