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Jiao Y, An L, Wang W, Ma J, Wu C, Wu X. Microbial communities and their roles in the Cenozoic sulfurous oil reservoirs in the Southwestern Qaidam Basin, Western China. Sci Rep 2023; 13:7988. [PMID: 37198206 DOI: 10.1038/s41598-023-33978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
The latest discovery of sulfurous natural gas marked a breakthrough in the Cenozoic natural gas exploration in the southwestern margin of Qaidam Basin. The 16S rRNA analyses were performed on the crude oil samples from H2S-rich reservoirs in the Yuejin, Shizigou and Huatugou profiles, to understand the sulfurous gas origin, which was also integrated with carbon and hydrogen isotopes of alkane and sulfur isotopes of H2S collected from the Yingxiongling Area. Results show that the microorganisms in samples can survive in the hypersaline reservoirs, and can be classified into multiple phyla, including Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Haloanaerobiaeota. Methanogens are abundant in all of the three profiles, while sulfate-reducing bacteria are abundant in Yuejin and Huatugou profiles, contributing to the methane and H2S components in the natural gas. The carbon, hydrogen and sulfur isotopes of sulfurous natural gas in the Yingxiongling Area show that the natural gas is a mixture of coal-type gas and oil-type gas, which was primarily derived from thermal degradation, and natural gas from the Yuejin and Huatugou profiles also originated from biodegradation. The isotopic analysis agrees well with the 16S rRNA results, i.e., H2S-rich natural gas from the Cenozoic reservoirs in the southwest margin of the Qaidam Basin was primarily of thermal genesis, with microbial genesis of secondary importance.
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Affiliation(s)
- Yue Jiao
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Liyun An
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Wei Wang
- The No. 1 Oil Extraction Plant, Qinghai Oilfield Company, PetroChina, Haixi, 817000, Qinghai, China
| | - Jian Ma
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Chaodong Wu
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China.
| | - Xiaolei Wu
- College of Engineering, Peking University, Beijing, 100871, China
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Ndlovu S, Suinyuy TN, Pérez-Fernández MA, Magadlela A. Encephalartos natalensis, Their Nutrient-Cycling Microbes and Enzymes: A Story of Successful Trade-Offs. PLANTS (BASEL, SWITZERLAND) 2023; 12:1034. [PMID: 36903894 PMCID: PMC10005579 DOI: 10.3390/plants12051034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Encephalartos spp. establish symbioses with nitrogen (N)-fixing bacteria that contribute to soil nutrition and improve plant growth. Despite the Encephalartos mutualistic symbioses with N-fixing bacteria, the identity of other bacteria and their contribution to soil fertility and ecosystem functioning is not well understood. Due to Encephalartos spp. being threatened in the wild, this limited information presents a challenge in developing comprehensive conservation and management strategies for these cycad species. Therefore, this study identified the nutrient-cycling bacteria in Encephalartos natalensis coralloid roots, rhizosphere, and non-rhizosphere soils. Additionally, the soil characteristics and soil enzyme activities of the rhizosphere and non-rhizosphere soils were assayed. The coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis were collected from a population of >500 E. natalensis in a disturbed savanna woodland at Edendale in KwaZulu-Natal (South Africa) for nutrient analysis, bacterial identification, and enzyme activity assays. Nutrient-cycling bacteria such as Lysinibacillus xylanilyticus; Paraburkholderia sabiae, and Novosphingobium barchaimii were identified in the coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis. Phosphorus (P) cycling (alkaline and acid phosphatase) and N cycling (β-(D)-Glucosaminidase and nitrate reductase) enzyme activities showed a positive correlation with soil extractable P and total N concentrations in the rhizosphere and non-rhizosphere soils of E. natalensis. The positive correlation between soil enzymes and soil nutrients demonstrates that the identified nutrient-cycling bacteria in E. natalensis coralloid roots, rhizosphere, and non-rhizosphere soils and associated enzymes assayed may contribute to soil nutrient bioavailability of E. natalensis plants growing in acidic and nutrient-poor savanna woodland ecosystems.
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Affiliation(s)
- Siphelele Ndlovu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Terence N. Suinyuy
- School of Biology and Environmental Sciences, University of Mpumalanga (Mbombela Campus), Private Bag X11283, Mbombela 1200, South Africa
| | - María A. Pérez-Fernández
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013 Seville, Spain
| | - Anathi Magadlela
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
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Gao J, Xie H. Daylily intercropping: Effects on soil nutrients, enzyme activities, and microbial community structure. FRONTIERS IN PLANT SCIENCE 2023; 14:1107690. [PMID: 36890887 PMCID: PMC9986260 DOI: 10.3389/fpls.2023.1107690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The daylily (Hemerocallis citrina Baroni)/other crop intercropping system can be a specific and efficient cropping pattern in a horticultural field. Intercropping systems contribute to the optimization of land use, fostering sustainable and efficient agriculture. In the present study, high-throughput sequencing was employed to explore the diversity in the root-soil microbial community in the intercropping of four daylily intercropping systems [watermelon (Citrullus lanatus)/daylily (WD), cabbage (Brassica pekinensis)/daylily (CD), kale (Brassica oleracea)/daylily (KD), watermelon/cabbage/kale/daylily (MI)], and determine the physicochemical traits and enzymatic activities of the soil. The results revealed that the contents of available potassium (2.03%-35.71%), available phosphorus (3.85%-62.56%), available nitrogen (12.90%-39.52%), and organic matter (19.08%-34.53%), and the urease (9.89%-31.02%) and sucrase (23.63%-50.60%) activities, and daylily yield (7.43%- 30.46%) in different intercropping soil systems were significantly higher compared to those in the daylily monocropping systems (CK). The bacterial Shannon index increased significantly in the CD and KD compared to the CK. In addition, the fungi Shannon index was also increased significantly in the MI, while the Shannon indices of the other intercropping modes were not significantly altered. Different intercropping systems also caused dramatic architectural and compositional alterations in the soil microbial community. A prominently higher relative richness of Bacteroidetes was noted in MI compared to that in CK, while Acidobacteria in WD and CD and Chloroflexi in WD were pronouncedly less abundant compared to those in CK. Furthermore, the association between soil bacteria taxa and soil characteristic parameters was stronger than that between fungi and soil. In conclusion, the present study demonstrated that the intercropping of daylily with other crops could significantly improve the nutrient levels of the soil and optimize the soil bacterial microflora composition and diversity.
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Stanek M, Kushwaha P, Murawska-Wlodarczyk K, Stefanowicz AM, Babst-Kostecka A. Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome. GEODERMA 2023; 430:116328. [PMID: 37600960 PMCID: PMC10438910 DOI: 10.1016/j.geoderma.2023.116328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.
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Affiliation(s)
- Małgorzata Stanek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Priyanka Kushwaha
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | | | - Anna M. Stefanowicz
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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Zhao Y, Li X, Li Y, Bao H, Nan J, Xu G. Rapid biodegradation of atrazine by a novel Paenarthrobacter ureafaciens ZY and its effects on soil native microbial community dynamic. Front Microbiol 2023; 13:1103168. [PMID: 36687626 PMCID: PMC9846760 DOI: 10.3389/fmicb.2022.1103168] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
An atrazine-utilizing bacterium, designated as ZY, was isolated from agricultural soil and identified as Paenarthrobacter ureafaciens. The P. ureafaciens ZY demonstrated a significant degradation capacity of atrazine, with the degradation efficiency of 12.5 mg L-1 h-1 in liquid media (at pH 7, 30°C, and the atrazine level of 100 mg L-1). The P. ureafaciens ZY contained three atrazine-degrading genes (i.e., trzN, atzB, and atzC) could metabolize atrazine to form cyanuric acid, which showed lower biotoxicity than the parent atrazine as predicted by Ecological Structure Activity Relationships model. A laboratory-scale pot experiment was performed to examine the degradation of atrazine by P. ureafaciens ZY inoculation and investigate its effects on the native microbial communities. The results exhibited that the P. ureafaciens ZY was conductive to the degradation of atrazine, increased the total soil phospholipid fatty acids at the atrazine level of 50, 70, and 100 mg kg-1. By using high-throughput sequencing analysis, Frateuria, Dyella, Burkholderia-Caballeronia-Paraburkholderia were considered as the most important indigenous atrazine-degrading microorganisms due to their relative abundances were positively correlated with the atrazine degradation rate. In addition, P. ureafaciens ZY also increased the abundance of atrazine-degrading genus Streptomyces and Bacillus, indicating that there may be a synergic relationship between them in the process of atrazine degradation. Our work provides a new insight between inoculums and native microorganisms on the degradation of atrazine.
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Affiliation(s)
- Yue Zhao
- School of Environment, Harbin Institute of Technology, Harbin, China
| | - Xin Li
- School of Environment, Harbin Institute of Technology, Harbin, China,*Correspondence: Xin Li,
| | - Yunyang Li
- School of Environment, Harbin Institute of Technology, Harbin, China
| | - Huanyu Bao
- School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jun Nan
- School of Environment, Harbin Institute of Technology, Harbin, China
| | - Guoren Xu
- School of Environment, Harbin Institute of Technology, Harbin, China,College of Resources and Environment, University of Chinese Academy of Sciences (UCAS), Beijing, China
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Chhetri G, Kim I, Kim J, So Y, Park S, Jung Y, Seo T. Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato). Front Microbiol 2023; 14:1140484. [PMID: 37082173 PMCID: PMC10110911 DOI: 10.3389/fmicb.2023.1140484] [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: 01/11/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T = TBRC 15696T).
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Response of root endosphere bacterial communities of typical rice cultivars to nitrogen fertilizer reduction at the jointing stage. Arch Microbiol 2022; 204:722. [DOI: 10.1007/s00203-022-03334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/16/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022]
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Bai YC, Li BX, Xu CY, Raza M, Wang Q, Wang QZ, Fu YN, Hu JY, Imoulan A, Hussain M, Xu YJ. Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities. Front Microbiol 2022; 13:852342. [PMID: 35369467 PMCID: PMC8971985 DOI: 10.3389/fmicb.2022.852342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut-tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut-tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.
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Affiliation(s)
- Yong-Chao Bai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bao-Xin Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | | | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qi-Zhu Wang
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Ya-Nan Fu
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Jian-Yang Hu
- State Key Laboratory of the Discovery and Development of Novel Pesticides, Shenyang Sinochem Agrochemicals R&D Co., Ltd., Shenyang, China
| | - Abdessamad Imoulan
- Department of Biology, Faculty of Science and Technics of Errachidia, Mouly Ismail University, Meknes, Morocco
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71. [PMID: 34596501 DOI: 10.1099/ijsem.0.004943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem,, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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de Lajudie P, Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020. Int J Syst Evol Microbiol 2021; 71:004784. [PMID: 33956594 PMCID: PMC8289204 DOI: 10.1099/ijsem.0.004784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/20/2021] [Indexed: 02/04/2023] Open
Affiliation(s)
- Philippe de Lajudie
- IRD, University of Montpellier, CIRAD, INRAE, SupAgro, LSTM, Montpellier, France
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Finland
- Department of Biology, University of Turku, Finland
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