151
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Jia T, Yao Y, Wang R, Wu T, Chai B. Dynamics Relationship of Phyllosphere and Rhizosphere Bacterial Communities During the Development of Bothriochloa ischaemum in Copper Tailings. Front Microbiol 2020; 11:869. [PMID: 32547500 PMCID: PMC7270166 DOI: 10.3389/fmicb.2020.00869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
Copper mining and the byproducts associated with the industry have led to serious pollution in the Loess Plateau of China. There is a potential in improving the ecological restoration efficiency of such degraded land through combining microbial and plant remediation approaches. However, the community structure and function of phyllosphere and rhizosphere microorganisms and their response to plant development in copper tailings dams are poorly understood. This study investigated the impact of the phyllosphere and rhizosphere microbial communities on Bothriochloa ischaemum during three distinct plant development stages: seedling, tiller, and mature. The relative species abundance and Shannon index of bacterial communities of the rhizosphere during the seedling and tiller stages were distinct from that in the mature stage. Dominant bacteria at the level of phyla, such as Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, followed distinct patterns associated with plant development in the phyllosphere, but the predominant bacteria were similar in the rhizosphere. Redundancy analysis showed that aboveground total nitrogen and the carbon and nitrogen ratio of this plant species significantly affected phyllosphere bacterial community structure, whereas soil water content, soil nutrients, electrical conductivity, and salinity significantly affected rhizosphere bacterial community structure. Moreover, keystone phyllosphere and rhizosphere bacterial species differed significantly. This study sheds new light on understanding the dynamic relationship of phyllosphere and rhizosphere bacterial communities during plant development in copper tailings. These results are beneficial to the development and utilization of beneficial microbial communities at different stages of development, which might help to reclaim and stabilize tailings more effectively.
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Affiliation(s)
- Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
- *Correspondence: Tong Jia,
| | - Yushan Yao
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Ruihong Wang
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, GA, United States
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
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152
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Huang G, Liao J, Han Z, Li J, Zhu L, Lyu G, Lu L, Xie Y, Ma J. Interaction between Fungal Communities, Soil Properties, and the Survival of Invading E. coli O157:H7 in Soils. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103516. [PMID: 32443436 PMCID: PMC7277763 DOI: 10.3390/ijerph17103516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 11/16/2022]
Abstract
Pathogens that invade into the soil cancontaminate food and water, andinfect animals and human beings. It is well documented that individual bacterial phyla are well correlated with the survival of E. coliO157 (EcO157), while the interaction betweenthe fungal communities and EcO157 survival remains largely unknown. In this study, soil samples from Tongliao, Siping, and Yanji in northeast China were collected and characterized. Total DNA was extracted for fungal and bacterial community characterization. EcO157 cells were spiked into the soils, and their survival behavior was investigated. Results showed that both fungal and bacterial communities were significantly correlated (p < 0.01) with the survival of EcO157 in soils, and the relative abundances of fungal groups (Dothideomycetes and Sordariomycetes) and some bacterial phyla (Acidobacteria, Firmicutes, gamma- and delta-Proteobacteria)weresignificantly correlated with ttds (p < 0.01). Soil pH, EC (electric conductance) salinity, and water-soluble nitrate nitrogen were significantly correlated with survival time (time to reach the detection limit, ttd) (p < 0.05). The structural equation model indicated that fungal communities could directly influence ttds, and soil properties could indirectly influence the ttds through fungal communities. The first log reduction time (δ) was mainly correlated with soil properties, while the shape parameter (p) was largely correlated with fungal communities. Our data indicated that both fungal and bacterial communities were closely correlated (p < 0.05)with the survival of EcO157 in soils, and different fungal and bacterial groups might play different roles. Fungal communities and bacterial communities explained 5.87% and 17.32% of the overall variation of survival parameters, respectively. Soil properties explained about one-third of the overall variation of survival parameters. These findings expand our current understanding of the environmental behavior of human pathogens in soils.
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Affiliation(s)
- Guannan Huang
- Key Laboratory of Ground Water Resource and Environment, Ministry of Education, Jilin University, Changchun 130021, China;
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Jiafen Liao
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (Z.H.); (J.L.)
| | - Jiahang Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (Z.H.); (J.L.)
| | - Liyue Zhu
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Guangze Lyu
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Lu Lu
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Yuang Xie
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
| | - Jincai Ma
- Key Laboratory of Ground Water Resource and Environment, Ministry of Education, Jilin University, Changchun 130021, China;
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; (J.L.); (L.Z.); (G.L.); (L.L.); (Y.X.)
- Correspondence: ; Tel.: +86-431-85168429
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153
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Gupta V, Singh I, Rasool S, Verma V. Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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154
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Zhang S, Wang Y, Sun L, Qiu C, Ding Y, Gu H, Wang L, Wang Z, Ding Z. Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation. BMC Microbiol 2020; 20:103. [PMID: 32349665 PMCID: PMC7191807 DOI: 10.1186/s12866-020-01794-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/19/2020] [Indexed: 11/13/2022] Open
Abstract
Background Different mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community structure and ecosystem function in tea plantation under different mulching patterns was limited. In this study, we investigated bacterial and fungal communities of tea plantation soils under polyethylene film and peanut hull mulching using high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing. Results The results showed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, and the dominant fungal phyla were Ascomycota, Mortierellomycota and Basidiomycota in all samples, but different mulching patterns affected the distribution of microbial communities. At the phylum level, the relative abundance of Nitrospirae in peanut hull mulching soils (3.24%) was significantly higher than that in polyethylene film mulching soils (1.21%) in bacterial communities, and the relative abundances of Mortierellomycota and Basidiomycota in peanut hull mulching soils (33.72, 21.93%) was significantly higher than that in polyethylene film mulching soils (14.88, 6.53%) in fungal communities. Peanut hull mulching increased the diversity of fungal communities in 0–20 cm soils and the diversity of bacterial communities in 20–40 cm soils. At the microbial functional level, there was an enrichment of bacterial functional features, including amino acid transport and metabolism and energy production and conversion, and there was an enrichment of fungal functional features, including undefined saprotrophs, plant pathogens and soils aprotrophs. Conclusions Unique distributions of bacterial and fungal communities were observed in soils under organic mulching. Thus, we believe that the organic mulching has a positive regulatory effect on the soil bacterial and fungal communities and ecosystem functions, and so, is more suitable for tea plantation.
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Affiliation(s)
- Shuning Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yiqian Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Honglian Gu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Linjun Wang
- Weihai agricultural and rural affairs service center, Weihai, 264200, Shandong, China
| | - Zhaoshun Wang
- Weihai agricultural and rural affairs service center, Weihai, 264200, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
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155
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The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere. Genes (Basel) 2020; 11:genes11040456. [PMID: 32331348 PMCID: PMC7230438 DOI: 10.3390/genes11040456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022] Open
Abstract
The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.
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156
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Zhang X, Li X, Zhao X, Chen X, Zhou B, Weng L, Li Y. Bioelectric field accelerates the conversion of carbon and nitrogen in soil bioelectrochemical systems. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121790. [PMID: 31818651 DOI: 10.1016/j.jhazmat.2019.121790] [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: 09/26/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Soil bioelectrochemical systems (BESs) utilize indigenous microorganisms to generate biocurrent/electric fields that stimulate the degradation of organic pollutants, exhibiting great potential in the removal of petroleum hydrocarbons from soils. In this study, a horizontal bioelectric field was constructed to investigate the conversion of carbon and nitrogen in a soil BES. After 182 days, the degradation rates of total petroleum hydrocarbons, alkanes, and aromatics were promoted by 52 %, 38% and 136%, respectively. Meanwhile, the bioelectric field accelerated NH4+-N production near the cathode, whereas NH4+-N consumption near the anode indicated that the bioelectric field promoted the cathode-dominated ammoniation process and the anode-dominated denitrification process. Additionally, a distinctive microbial community was formed under the bioelectric field, and the improved degradation on the cathode and the anode relied on special functional bacteria (typically, cathode, Alcanivorax; anode, Marinobacter). The dramatic enrichment in anodic denitrifying bacteria, including Pontibacillus, Sediminimonas, Georgenia, etc., explained the enhanced denitrification process under the bioelectric field. This study simultaneously clarified the carbon and nitrogen conversion processes and corresponding bacterial community occurring under the bioelectric field for the first time, helping to form regulation strategies in the practical application of soil BESs and providing a new perspective for removing petroleum hydrocarbons from soils.
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Affiliation(s)
- Xiaolin Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China.
| | - Xiaodong Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Xiaodong Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Bin Zhou
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Liping Weng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yongtao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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157
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Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil. Microorganisms 2020; 8:microorganisms8030442. [PMID: 32245141 PMCID: PMC7143980 DOI: 10.3390/microorganisms8030442] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soils. As is the case for other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and can improve their growth. This study was conducted to isolate, identify, and characterize selected PGP properties of these three functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. The bacteria were isolated based on their colonial growth on respective functional media, identified using both molecular and selected biochemical properties, and were assessed for their functional quantitative activities as well as PGP properties based on seed germination tests and indole-3-acetic acid (IAA) production. Out of the 15 identified bacterial isolates that exhibited beneficial phenotypic traits, a third belong to the genus Burkholderia and a fifth to Stenotrophomonas sp., with both genera consisting of members from two different functional groups. The results of the experiments confirm the multiple PGP traits of some selected bacterial isolates based on their respective high functional activities, root and shoot lengths, and seedling vigor improvements when bacterized on mung bean seeds, as well as significant IAA production. The results of this study suggest that these functional bacterial strains could potentially be included in bio-fertilizer formulations for crop growth on acid soils.
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158
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Tang A, Haruna AO, Majid NMA, Jalloh MB. Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil. Microorganisms 2020; 8:microorganisms8030442. [PMID: 32245141 DOI: 10.1101/351916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 05/22/2023] Open
Abstract
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soils. As is the case for other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and can improve their growth. This study was conducted to isolate, identify, and characterize selected PGP properties of these three functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. The bacteria were isolated based on their colonial growth on respective functional media, identified using both molecular and selected biochemical properties, and were assessed for their functional quantitative activities as well as PGP properties based on seed germination tests and indole-3-acetic acid (IAA) production. Out of the 15 identified bacterial isolates that exhibited beneficial phenotypic traits, a third belong to the genus Burkholderia and a fifth to Stenotrophomonas sp., with both genera consisting of members from two different functional groups. The results of the experiments confirm the multiple PGP traits of some selected bacterial isolates based on their respective high functional activities, root and shoot lengths, and seedling vigor improvements when bacterized on mung bean seeds, as well as significant IAA production. The results of this study suggest that these functional bacterial strains could potentially be included in bio-fertilizer formulations for crop growth on acid soils.
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Affiliation(s)
- Amelia Tang
- Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu 97008, Sarawak, Malaysia
| | - Ahmed Osumanu Haruna
- Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu 97008, Sarawak, Malaysia
- Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nik Muhamad Ab Majid
- Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mohamadu Boyie Jalloh
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Sandakan Branch, Locked Bag No. 3, Sandakan 90509, Sabah, Malaysia
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159
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Zhang H, Huang M, Zhang W, Gardea-Torresdey JL, White JC, Ji R, Zhao L. Silver Nanoparticles Alter Soil Microbial Community Compositions and Metabolite Profiles in Unplanted and Cucumber-Planted Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3334-3342. [PMID: 32088952 DOI: 10.1021/acs.est.9b07562] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The rapid development of nanotechnology makes the environmental impact assessment a necessity to ensure the sustainable use of engineered nanomaterials. Here, silver nanoparticles (AgNPs) at 100 mg/kg were added to soils in the absence or presence of cucumber (Cucumis sativa) plants for 60 days. The response of the soil microbial community and associated soil metabolites was investigated by 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics, respectively. The results show that AgNP exposure significantly increased the soil pH in both unplanted and cucumber-planted soils. The soil bacterial community structure was altered upon Ag exposure in both soils. Several functionally significant bacterial groups, which are associated with carbon, nitrogen, and phosphorus cycling, were compromised by AgNPs in both unplanted and cucumber-planted soils. Generally, plants played a limited role in mediating the impact of AgNPs on the bacterial community. Soil metabolomic analysis showed that AgNPs altered the metabolite profile in both unplanted and cucumber-planted soils. The significantly changed metabolites are involved in sugar and amino acid-related metabolic pathways, indicating the perturbation of C and N metabolism, which is consistent with the bacterial community structure results. In addition, several fatty acids were significantly decreased upon exposure to AgNPs in both unplanted and cucumber-planted soils, suggesting the possible oxidative stress imposed on microbial cell membranes. These results provide valuable information for understanding the biological and biochemical impact of AgNP exposure on both plant species and on soil microbial communities; such understanding is needed to understand the risk posed by these materials in the environment.
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Affiliation(s)
- Huiling Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Min Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Wenhui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jorge L Gardea-Torresdey
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jason C White
- Analytical Chemistry, The Connecticut Agricultural Experiment Station (CAES), New Haven, Connecticut 06504, United States
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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160
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Lopez S, van der Ent A, Sumail S, Sugau JB, Buang MM, Amin Z, Echevarria G, Morel JL, Benizri E. Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia). Environ Microbiol 2020; 22:1649-1665. [PMID: 32128926 DOI: 10.1111/1462-2920.14970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 12/01/2022]
Abstract
The Island of Borneo is a major biodiversity hotspot, and in the Malaysian state of Sabah, ultramafic soils are extensive and home to more than 31 endemic nickel hyperaccumulator plants. The aim of this study was to characterize the structure and the diversity of the rhizosphere bacterial communities of several of these nickel hyperaccumulator plants and factors that affect these bacterial communities in Sabah. The most abundant phyla were Proteobacteria, Acidobacteria and Actinobacteria. At family level, Burkholderiaceae and Xanthobacteraceae (Proteobacteria phylum) were the most abundant families in the hyperaccumulator rhizospheres. Redundancy analysis based on soil chemical analyses and relative abundances of the major bacterial phyla showed that abiotic factors of the studied sites drove the bacterial diversity. For all R. aff. bengalensis rhizosphere soil samples, irrespective of studied site, the bacterial diversity was similar. Moreover, the Saprospiraceae family showed a high representativeness in the R. aff. bengalensis rhizosphere soils and was linked with the nickel availability in soils. The ability of R. aff. bengalensis to concentrate nickel in its rhizosphere appears to be the major factor driving the rhizobacterial community diversity unlike for other hyperaccumulator species.
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Affiliation(s)
- Séverine Lopez
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
| | - Antony van der Ent
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France.,Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, St Lucia, 4072, QLD, Australia
| | | | | | - Matsain Mohd Buang
- Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia
| | - Zarina Amin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Guillaume Echevarria
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France.,Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Jean Louis Morel
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
| | - Emile Benizri
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000, Nancy, France
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161
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Yan C, Huang J, Cao C, Li R, Ma Y, Wang Y. Effects of PVP-coated silver nanoparticles on enzyme activity, bacterial and archaeal community structure and function in a yellow-brown loam soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:8058-8070. [PMID: 31897981 DOI: 10.1007/s11356-019-07347-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
The undesirable effects of silver nanoparticles (AgNPs) on soil environment have caused much concern. The previous studies, however, focused on sandy soil, with little known on others. In present study, the effects of polyvinylpyrrolidone-coated AgNPs (0, 1, 10, and 100 mg kg- 1 soil) on enzyme activities (urease and dehydrogenase), ammonia-oxidizing bacteria (AOB) and archaea (AOA), bacterial and archaeal communities, and microbial function profile in a yellow-brown loam soil were investigated. The significant dose-response inhibitions of AgNPs on enzyme activities were observed, with dehydrogenase more susceptible to AgNPs. Both of bacterial and archaeal amoA genes were reduced by AgNPs above 10 mg kg- 1, with AOB more susceptible to AgNPs than AOA. AgNPs at 100 mg kg- 1 caused reductions on the dominant Nitrosospira and Nitrosomonas, and even disappearance on Nitrosovibrio, while increase on Nitrososphaera significantly. AgNPs also changed bacterial and archaeal community structure. Exposure to AgNPs at 100 mg kg- 1 caused significant increases by 186.79% and 44.89% for Bacteroidetes and Proteobacteria, while decreases by 47.82%, 44.09%, 43.67%, and 80.44% for Actinobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia, respectively. Moreover, three dominant archaeal phyla (Thaumarchaeota, Euryarchaeota, and Parvarchaeota) were also reduced in the presence of AgNPs, especially Thaumarchaeota with the significant reduction of 13.71%. PICRUSt prediction revealed that AgNPs indeed had the potential to change soil microbial community's functional contributions. It must be cautious on the interference of AgNPs to soil ecological functions in the future.
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Affiliation(s)
- Chunni Yan
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China.
| | - Chong Cao
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Runqing Li
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yixuan Ma
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yaoyao Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
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162
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Liu X, Wang Y, Liu Y, Chen H, Hu Y. Response of Bacterial and Fungal Soil Communities to Chinese Fir ( Cunninghamia lanceolate) Long-Term Monoculture Plantations. Front Microbiol 2020; 11:181. [PMID: 32184765 PMCID: PMC7058989 DOI: 10.3389/fmicb.2020.00181] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/24/2020] [Indexed: 11/30/2022] Open
Abstract
Successive rotation and monoculture, as common silvicultural practices, are extensively applied worldwide, particularly in subtropical Chinese fir (Cunninghamia lanceolata) plantations in southern China. Although regeneration failure and productivity decline are frequently observed in continuous monoculture plantations, the potential mechanisms are still unclear. In this study, high-throughput sequencing was used to compare the diversity and composition of bacterial and fungal communities among different generations of Chinese fir plantation (first rotation, FRP; second rotation, SRP; third rotation, TRP) and natural forest (NF) in December and June. Our results showed significant declines in richness and diversity of bacterial and fungal communities in TRP compared with FRP and SRP, but no significant difference between FRP and SRP. The fungal phyla with high relative abundance were Basidiomycota (12.9-76.9%) and Ascomycota (14.3-52.8%), while the bacterial phyla with high relative abundance were Acidobacteria (39.1-57.7%) and Proteobacteria (21.2-39.5%) in all treatments at both sampling months. On average, the relative abundance of Basidiomycota in TRP increased by 53.4%, while that of Ascomycota decreased by 37.1% compared with FRP and SRP. Moreover, soil NH4 +-N, pH, and DOC appear to be the key factors in shaping the fungal communities, while soil NH4 +-N, DOCN, and AP primarily drive the changes in bacterial communities. Collectively, our findings highlighted the alteration of soil bacterial and fungal communities induced by changes in soil nutrient environment in different generations of continuously cultivated Chinese fir plantation.
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Affiliation(s)
- Xian Liu
- Forest Ecology and Stable Isotope Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuzhe Wang
- Forest Ecology and Stable Isotope Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhui Liu
- Xinkou Forest Farm, Fujian Agriculture and Forestry University, Sanming, China
| | - Hui Chen
- Xinkou Forest Farm, Fujian Agriculture and Forestry University, Sanming, China
| | - Yalin Hu
- Forest Ecology and Stable Isotope Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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163
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Hui C, Jiang H, Liu B, Wei R, Zhang Y, Zhang Q, Liang Y, Zhao Y. Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:136003. [PMID: 31846813 DOI: 10.1016/j.scitotenv.2019.136003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/20/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Chitin amendment is a promising agricultural management strategy to control fungal and nematodal plant diseases and to improve crop yield. Chitin degradation in the soil contributes significantly to carbon and nitrogen cycling in terrestrial ecosystems. However, little is known about chitin degradation and bacterial chitinolytic communities in agricultural soil under different fertilization regimes. Thus, in the present study, a 42-day soil incubation experiment was conducted, in which soil under four fertilization regimes (i.e., no fertilization (CK), chemical fertilizer (CF), pig manure plus 50% chemical fertilizer (PMCF), and rice straw plus 100% chemical fertilizer (SRCF)) were amended or not with chitin or its monomer, N-acetylglucosamine (NAG). Different nitrogen forms and CO2 and N2O emission were measured to evaluate chitin degradation and its environmental implications. SRCF soil had the highest CO2 emission, chitin N mineralization, and fungal abundance. NAG and chitin were enriched to exploit the chitin degraders. High-throughput sequencing analyses reveled that Streptomycetaceae, Oxalobacteraceae, Gemmatimonadaceae, and Acidobacteria were generally increased upon chitin amendment in CK, CF, and PMCF soil, whereas Streptomycetaceae dominated chitin-amended SRCF soil. Herpetosiphonaceae was enriched only in chitin-amended CK soil. LEfSe and network analysis were used to predict chitinolytic and opportunistic species, and revealed that most previously reported chitinolytic bacteria were detected in the present study and new potential chitin degraders, including unidentified_Solibacterales, Gemmatimonadaceae, and Herpetosiphonaceae, were identified. Some members of Firmicutes, Actinobacteria, and Proteobacteria, including Bacillus, and Kitasatospora, were speculated to be opportunistic species. The findings improve our understanding of the effects of chitin degradation on carbon and nitrogen cycling in agricultural soil under different fertilization regimes and help to identify chitinolytic bacteria.
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Affiliation(s)
- Cai Hui
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hui Jiang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bing Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ran Wei
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yiping Zhang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qichun Zhang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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164
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Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
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165
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Manpoong C, De Mandal S, Bangaruswamy DK, Perumal RC, Benny J, Beena P, Ghosh A, Kumar NS, Tripathi SK. Linking rhizosphere soil biochemical and microbial community characteristics across different land use systems in mountainous region in Northeast India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100625] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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166
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One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil. Microbiol Resour Announc 2020; 9:9/5/e01087-19. [PMID: 32001557 PMCID: PMC6992861 DOI: 10.1128/mra.01087-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.
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167
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Fang W, Wang X, Huang B, Zhang D, Liu J, Zhu J, Yan D, Wang Q, Cao A, Han Q. Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109850. [PMID: 31677569 DOI: 10.1016/j.ecoenv.2019.109850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/28/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.
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Affiliation(s)
- Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China.
| | - Qingli Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, 650224, China
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168
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Griffin JS, Haug LA, Rivera VA, Gonzalez LMH, Kelly JJ, Miller WM, Wells GF, Packman AI. Soil hydrology drives ecological niche differentiation in a native prairie microbiome. FEMS Microbiol Ecol 2020; 96:5593953. [PMID: 31626296 DOI: 10.1093/femsec/fiz163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/16/2019] [Indexed: 11/14/2022] Open
Abstract
While the impacts of soil moisture on soil microbiome diversity and composition are well characterized, the influence of hydrological regime has been overlooked. As precipitation patterns are altered by climate change, understanding the impact of soil hydrology on community structure and function is critical. In this work, water level was continuously monitored for over a year in a Midwestern prairie-wetland at 10 cm depth increments up to a depth of 120 cm in 10 locations. We analyzed microbiome composition and edaphic factors in soil cores collected from this unique spatially distributed, longitudinal data set. We demonstrate that the fraction of time that each sample was inundated explains more variability in diversity and composition across this site than other commonly assessed edaphic factors, such as soil pH or depth. Finally, we show that these compositional changes influence abundance of ammonia oxidizers. The observed patterns in community composition and diversity are fundamentally regulated by the interaction of water with a structured landscape, particularly an elevated sand ridge characterized by drier conditions and a lower-lying wetland with more clayey soils. Similar processes are generally expected to influence the biogeography of many terrestrial environments, as morphology, hydrology and soil properties generally co-vary.
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Affiliation(s)
- James S Griffin
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Loren A Haug
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Vivien A Rivera
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Liliana M Hernandez Gonzalez
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - John J Kelly
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd., Chicago, IL 60660, USA
| | - William M Miller
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Aaron I Packman
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA
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169
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Huang XF, Li SQ, Li SY, Ye GY, Lu LJ, Zhang L, Yang LY, Qian X, Liu J. The effects of biochar and dredged sediments on soil structure and fertility promote the growth, photosynthetic and rhizosphere microbial diversity of Phragmites communis (Cav.) Trin. ex Steud. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134073. [PMID: 31473547 DOI: 10.1016/j.scitotenv.2019.134073] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/05/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
The improvement of urban river revetment soil is conducive to promote the growth of pioneer plants which can accelerate the restoration of ecosystems. How to effectively amend soil structure and composition to provide a suitable soil rhizosphere for rapid plant expansion is essential to be solved in the study. Biochar and lake dredged sediments were used to amend an urban river bank soil, where compaction and lack of mineral nutrition hindered the growth of Phragmites. The study found that the addition of 50% mass of dredged sediments combined with 5% mass of straw biochar increased the plant height maximum growth rate, tiller number per unit area, and root biomass by 32.93%, 29.62%, and 41.39%, respectively. The reason for these positive effects on plant growth mainly involved the improvement of rhizosphere soil properties. Addition of biochar increased porosity and available phosphorus content while dredged sediments increased soil organic carbon, thereby increasing the underground unit total phosphorus content of Phragmites by 18.18%. An increase of the Alpha diversity index of rhizosphere microorganisms (8.18%) and the decrease in infection rate of arbuscular mycorrhizal fungi (23.61%) also proved that the rapid expansion of Phragmites was improved owing to changes of the soil physicochemical properties. The combination of biochar and dredged sediments realized synergistic improvement of soil physical structure and increase of nutrient content, which helped promote the growth and expansion of the underground part of Phragmites. This cost-effective method can be feasible used for improvement of urban river revetment ecosystem.
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Affiliation(s)
- Xiang-Feng Huang
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Shuang-Qiang Li
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Shi-Yang Li
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Guang-Yu Ye
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Li-Jun Lu
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Lin Zhang
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Liu-Yan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xin Qian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jia Liu
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
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170
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Li W, Liu X, Niu S. Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands. PeerJ 2019; 7:e8047. [PMID: 31844567 PMCID: PMC6911345 DOI: 10.7717/peerj.8047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/16/2019] [Indexed: 11/25/2022] Open
Abstract
Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
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Affiliation(s)
- Weike Li
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China.,Fire Engineering, China Fire and Rescue Institute, Beijing, China
| | - Xiaodong Liu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
| | - Shukui Niu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
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171
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Structure-function insights into elusive Mycobacterium tuberculosis protein Rv1916. Int J Biol Macromol 2019; 141:927-936. [PMID: 31505209 DOI: 10.1016/j.ijbiomac.2019.09.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/23/2019] [Accepted: 09/05/2019] [Indexed: 11/21/2022]
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide. Long duration of TB therapy, results in the persistence and development of drug resistant strains of causative organism Mycobacterium tuberculosis (Mtb). Novel drug targets against persistent Mtb is an immediate need for overcoming this global menace. Isocitrate lyase (ICL), the first enzyme of glyoxylate pathway, is essential for persistent Mtb and absent in humans, hence a propitious target for drug development. Pathogenic Mtb H37Rv, have two types of ICLs - ICL1 encoded by icl (Rv0467) is well characterized and homologous to eubacterial enzyme whereas ICL2 encoded by aceA is more related to eukaryotic isocitrate lyase. To compound it, the aceA gene is split into two ORFs namely rv1915/aceAa and rv1916/aceAb. No translational product has been reported for the later and therefore, in vivo existence of Rv1916/ICL2b is debatable. This study reports recombinant production of Rv1916 in heterologous host E. coli BL21 (DE3) for structure function studies. The studies categorically demonstrate that akin to Mtb ICL1, recombinant Rv1916 also possess dual ICL and methylisocitrate lyase (MICL) activities in vitro. Based on in silico analysis, a putative function linked to secondary metabolite synthesis is assigned to unique mycobacterial domain IV.
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172
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Liming Positively Modulates Microbial Community Composition and Function of Sugarcane Fields. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9120808] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liming combined with an optimum quantity of inorganic fertilizer, as a soil amendment in intensive agriculture, is a viable agricultural practice in terms of improving soil nutrient status and productivity, as well as mitigating soil degradation. The chief benefits of this strategy are fundamentally dependent on soil microbial function. However, we have limited knowledge about lime’s effects on soil microbiomes and their functions, nor on its comprehensive influence on soil nutrient status and the productivity of sugarcane plantations. This study compares the impacts of lime application (1-year lime (L1), 2-year lime (L2), and no lime (CK) on microbial communities, their functions, soil nutrient status, and crop yield in a sugarcane cropping system. We employed Illumina sequencing and functional analysis (PICRUSt and FUNGuild) to decipher microbial communities and functions. In comparison with CK, lime application (L1 and L2) mitigated soil acidity, increased the level of base cations (Ca2+ and Mg2+), and improved soil nutrient status (especially through N and P) as well as soil microbial functions associated with nutrient cycling and that are beneficial to plants, thereby improving plant agronomic parameters and yield. Liming (L1 and L2) increased species richness and stimulated an abundance of Acidobacteria and Chloroflexi compared to CK. In comparison with CK, the two functional categories related to metabolism (amino acid and carbohydrate) increased in the L1 field, whereas cofactors and vitamin metabolites increased in the L2 field. Turning to fungi, compared to CK, liming enriched symbiotrophs (endophytes, ectomycorrhizae, and arbuscular mycorrhizae) and led to a reduction of saprotrophs (Zygomycota and wood saprotrophs) and pathotrophs. The observed benefits of liming were, in turn, ultimately reflected in improved sugarcane agronomic performance, such as increased stalk height and weight in the sugarcane planting system. However, the increase in the above-mentioned parameters was more prominent in the L2 field compared to the L1 field, suggesting consecutive liming could be a practical approach in terms of sustainable production of sugarcane.
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173
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Anastopoulos I, Omirou M, Stephanou C, Oulas A, Vasiliades MA, Efstathiou AM, Ioannides IM. Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N 2O emissions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109389. [PMID: 31499464 DOI: 10.1016/j.jenvman.2019.109389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO2 and N2O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N2O emissions when treated with agricultural wastes. The highest soil direct N2O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N2O emissions. On the contrary, agricultural wastes stimulated CO2 accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N2O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N2O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N2O emissions.
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Affiliation(s)
| | - Michalis Omirou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus.
| | - Coralea Stephanou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus
| | - Anastasios Oulas
- Cyprus Institute of Neurology and Genetics, Bioinformatics Group, Cyprus
| | - Michalis A Vasiliades
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
| | - Angelos M Efstathiou
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
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174
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Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4943150. [PMID: 31815142 PMCID: PMC6878781 DOI: 10.1155/2019/4943150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/05/2022]
Abstract
To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.
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175
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Zhai Y, Hunting ER, Liu G, Baas E, Peijnenburg WJGM, Vijver MG. Compositional alterations in soil bacterial communities exposed to TiO 2 nanoparticles are not reflected in functional impacts. ENVIRONMENTAL RESEARCH 2019; 178:108713. [PMID: 31518961 DOI: 10.1016/j.envres.2019.108713] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 05/23/2023]
Abstract
Titanium dioxide nanoparticles (TiO2NP) are increasingly released in soil ecosystems, while there is limited understanding of the impacts of TiO2NP on soil bacterial communities. Here we investigated the effects of TiO2NP on the taxonomic composition and functional profile of a soil bacterial community over a 60-day exposure period. In short-term exposure (1-day), contradictory effects on the taxonomic composition of soil bacterial communities were found after exposure to a low realistic environmental concentration of TiO2NP at 1 mg/kg as compared to the effects induced by medium and high concentrations of TiO2NP at 500 and 2000 mg/kg. After long-term exposure (60-day), the negative effects of TiO2NP at the low concentration disappeared, and the inhibition by TiO2NP of the abundance of core taxa was enhanced along with increasing exposure concentrations. However, although significant alterations were observed in the taxonomic composition over time and exposure concentrations, no significant change was observed in the community functional profile as well as enzyme activity after 60-day exposure, indicating that functional redundancy likely contributed to the bacterial community tolerance after the exposure to TiO2NP. Our study highlighted the importance of assessing bacterial community compositional and functional responses in assessing the environmental risk of nanoparticles on soil ecosystems.
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Affiliation(s)
- Yujia Zhai
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands.
| | - Ellard R Hunting
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600GA, Delft, the Netherlands.
| | - Elise Baas
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands; National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands
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176
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Kobayashi K, Aoyagi H. Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP. PeerJ 2019; 7:e7876. [PMID: 31681511 PMCID: PMC6824334 DOI: 10.7717/peerj.7876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 09/12/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. METHODS In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. RESULTS At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively. DISCUSSION Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.
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Affiliation(s)
- Kazuki Kobayashi
- Division of Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideki Aoyagi
- Division of Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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177
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Jones JM, Heath KD, Ferrer A, Brown SP, Canam T, Dalling JW. Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes. FEMS Microbiol Ecol 2019; 95:5184448. [PMID: 30445583 DOI: 10.1093/femsec/fiy223] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/13/2018] [Indexed: 01/01/2023] Open
Abstract
Wood decomposition, a critical process in carbon and nutrient cycles, is influenced by environmental conditions, decomposer communities and substrate composition. While these factors differ between land and stream habitats, across-habitat comparisons of wood decay processes are rare, limiting our ability to evaluate the context- dependency of the drivers of decay. Here we tracked wood decomposition of three tree species placed in stream and terrestrial habitats in a lowland tropical forest in Panama. At 3 and 11 months we measured mass loss, wood nitrogen and wood polymer concentrations, and sampled wood-associated fungal and bacterial communities. After 11 months of decay we found that mass loss occurred 9% faster in streams than on land, but loss of cellulose, hemicellulose and lignin did not differ between habitats. We also observed large differences in microbial decomposer communities between habitats. Overall, we found faster mass loss of wood in water, but no differences in biotic decay processes between habitats despite distinct microbial communities in streams and on land. Our research challenges the assumption that wood decays relatively slowly in water reflecting unfavorable environmental conditions and a limited capacity of aquatic microbial communities to effectively degrade wood polymers.
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Affiliation(s)
- Jennifer M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shawn P Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN 38152, USA
| | - Thomas Canam
- Department of Biology, Eastern Illinois University, Charleston, IL 61920, USA
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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178
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Lusa M, Knuutinen J, Lindgren M, Virkanen J, Bomberg M. Microbial communities in a former pilot-scale uranium mine in Eastern Finland - Association with radium immobilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:619-640. [PMID: 31185409 DOI: 10.1016/j.scitotenv.2019.05.432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/09/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
The bacterial, fungal and archaeal communities were characterized in 17 top soil organic and mineral layer samples and in top sediment samples of the Paukkajanvaara area, a former pilot-scale uranium mine, located in Eno, Eastern Finland, using amplicon sequencing and qPCR. Soil and sediment samples were in addition analyzed for radium (226Ra), sulfate (SO42-), nitrate (NO3-) and phosphate (PO43-) concentrations. New bacterial strains, representing Pseudomonas spp., were isolated from the mine and reference area and used in laboratory experiments on uptake and leaching of radium (Ra). The effect of these strains on the sulfate leaching from the soil samples was also tested in vitro. Between 6 × 106 and 5 × 108 copies g-1 DW (dry weight) of bacterial 16S rRNA genes, 5 × 105-1 × 108 copies g-1 DW archaeal 16S rRNA genes and 1 × 105-1 × 108 copies g-1 DW fungal 5.8S rRNA genes were detected in the samples. A total of 814, 54 and 167 bacterial, archaeal and fungal genera, respectively, were identified. Proteobacteria, Euryarchaeota and Mortiriella were the dominant bacterial, archaeal and fungal phyla, respectively. All tested Pseudomonas spp. strains isolates from Paukkajanvaara removed Ra from the solution, but the amount of removed Ra depended on incubation conditions (temperature, time and nutrient broth). The highest removal of Ra (5320 L/kg DW) was observed by the Pseudomonas sp. strain T5-6-I at 37 °C. All Pseudomonas spp. strains decreased the release of Ra from soil with an average of 23% while simultaneously increasing the concentration of SO42- in the solution by 11%. As Pseudomonas spp. were frequent in both the sequence data and the cultures, these bacteria may play an important role in the immobilization of Ra in the Paukkajanvaara mine area.
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Affiliation(s)
- Merja Lusa
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland.
| | - Jenna Knuutinen
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland
| | - Marcus Lindgren
- Department of Chemistry, Radiochemistry, Faculty of Science, University of Helsinki, Finland
| | - Juhani Virkanen
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, Espoo, Finland
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179
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Wang B, Wang Y, Cui X, Zhang Y, Yu Z. Bioconversion of coal to methane by microbial communities from soil and from an opencast mine in the Xilingol grassland of northeast China. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:236. [PMID: 31624498 PMCID: PMC6781394 DOI: 10.1186/s13068-019-1572-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/21/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND The Xilingol grassland ecosystem has abundant superficial coal reserves. Opencast coal mining and burning of coal for electricity have caused a series of environmental challenges. Biogenic generation of methane from coal possesses the potential to improve economic and environmental outcomes of clean coal utilization. However, whether the microbes inhabiting the grassland soil have the functional potential to convert coal into biomethane is still unclear. RESULTS Microbial communities in an opencast coal mine and in grassland soil covering and surrounding this mine and their biomethane production potential were investigated by Hiseq sequencing and anaerobic cultivation. The microbial communities in covering soil showed high similarity to those in the surrounding soil, according to the pairwise weighted UniFrac distances matrix. The majority of bacterial communities in coal and soil samples belonged to the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. The dominant bacterial genera in grassland soil included Gaiella, Solirubrobacter, Sphingomonas and Streptomyces; whereas, the most abundant genus in coal was Pseudarthrobacter. In soil, hydrogenotrophic Methanobacterium was the dominant methanogen, and this methanogen, along with acetoclastic Methanosarcina and methylotrophic Methanomassiliicoccus, was detected in coal. Network-like Venn diagram showed that an average of 28.7% of microbial communities in the samples belonged to shared genera, indicating that there is considerable microbial overlap between coal and soil samples. Potential degraders and methanogens in the soil efficiently stimulated methane formation from coal samples by the culturing-based approach. The maximum biogenic methane yields from coal degradation by the microbial community cultured from grassland soil reached 22.4 μmol after 28 day. CONCLUSION The potential microbial coal degraders and methanogenic archaea in grassland soil were highly diverse. Significant amounts of biomethane were generated from coal by the addition of grassland soil microbial communities. The unique species present in grassland soil may contribute to efficient methanogenic coal bioconversion. This discovery not only contributes to a better understanding of global microbial biodiversity in coal mine environments, but also makes a contribution to our knowledge of the synthetic microbiology with regard to effective methanogenic microbial consortia for coal degradation.
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Affiliation(s)
- Bobo Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yanfen Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yiming Zhang
- Beijing Municipal Ecological Environment Bureau, Beijing, 100048 People’s Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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180
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Imchen M, Kumavath R, Vaz ABM, Góes-Neto A, Barh D, Ghosh P, Kozyrovska N, Podolich O, Azevedo V. 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages. Front Microbiol 2019; 10:2103. [PMID: 31616390 PMCID: PMC6764247 DOI: 10.3389/fmicb.2019.02103] [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: 06/10/2019] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Aline B M Vaz
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Natalia Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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181
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Kaestli M, O’Donnell M, Rose A, Webb JR, Mayo M, Currie BJ, Gibb K. Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia. PLoS Negl Trop Dis 2019; 13:e0007672. [PMID: 31487283 PMCID: PMC6728021 DOI: 10.1371/journal.pntd.0007672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
In the wet-dry tropics of Northern Australia, drinking water in remote communities is mostly sourced from bores accessing groundwater. Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season. Therefore, environmental bacteria such as iron-cycling bacteria promoting biofilm formation in pipes or opportunistic pathogens can occur in these waters. An opportunistic pathogen endemic to northern Australia and Southeast Asia and emerging worldwide is Burkholderia pseudomallei. It causes the frequently fatal disease melioidosis in humans and animals. As we know very little about the microbial composition of drinking water in remote communities, this study aimed to provide a first snapshot of the microbiota and occurrence of opportunistic pathogens in bulk water and biofilms from the source and through the distribution system of three remote water supplies with varying iron levels. Using 16s-rRNA gene sequencing, we found that the geochemistry of the groundwater had a substantial impact on the untreated microbiota. Different iron-cycling bacteria reflected differences in redox status and nutrients. We cultured and sequenced B. pseudomallei from bores with elevated iron and from a multi-species biofilm which also contained iron-oxidizing Gallionella, nitrifying Nitrospira and amoebae. Gallionella are increasingly used in iron-removal filters in water supplies and more research is needed to examine these interactions. Similar to other opportunistic pathogens, B. pseudomallei occurred in water with low organic carbon levels and with low heterotrophic microbial growth. No B. pseudomallei were detected in treated water; however, abundant DNA of another opportunistic pathogen group, non-tuberculous mycobacteria was recovered from treated parts of one supply. Results from this study will inform future studies to ultimately improve management guidelines for water supplies in the wet-dry tropics.
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Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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182
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Nasir F, Shi S, Tian L, Chang C, Ma L, Li X, Gao Y, Tian C. Strigolactones shape the rhizomicrobiome in rice (Oryza sativa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:118-133. [PMID: 31300137 DOI: 10.1016/j.plantsci.2019.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 05/03/2023]
Abstract
The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter, were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice.
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Affiliation(s)
- Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China.
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. MICROBIOME 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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184
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Huang L, Zhang H, Wu P, Entwistle S, Li X, Yohe T, Yi H, Yang Z, Yin Y. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res 2019; 46:D516-D521. [PMID: 30053267 PMCID: PMC5753378 DOI: 10.1093/nar/gkx894] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
Carbohydrate-active enzyme (CAZymes) are not only the most important enzymes for bioenergy and agricultural industries, but also very important for human health, in that human gut microbiota encode hundreds of CAZyme genes in their genomes for degrading various dietary and host carbohydrates. We have built an online database dbCAN-seq (http://cys.bios.niu.edu/dbCAN_seq) to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes. Compared to the other CAZyme resources, dbCAN-seq has the following new features: (i) a convenient download page to allow batch download of all the sequence and annotation data; (ii) an annotation page for every CAZyme to provide the most comprehensive annotation data; (iii) a metadata page to organize the bacterial genomes according to species metadata such as disease, habitat, oxygen requirement, temperature, metabolism; (iv) a very fast tool to identify physically linked CAZyme gene clusters (CGCs) and (v) a powerful search function to allow fast and efficient data query. With these unique utilities, dbCAN-seq will become a valuable web resource for CAZyme research, with a focus complementary to dbCAN (automated CAZyme annotation server) and CAZy (CAZyme family classification and reference database).
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Affiliation(s)
- Le Huang
- College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Han Zhang
- College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Peizhi Wu
- College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Sarah Entwistle
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Xueqiong Li
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Tanner Yohe
- Department of Computer Science, Northern Illinois University, DeKalb, IL, USA
| | - Haidong Yi
- College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Zhenglu Yang
- College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
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185
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Liddicoat C, Weinstein P, Bissett A, Gellie NJC, Mills JG, Waycott M, Breed MF. Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health? ENVIRONMENT INTERNATIONAL 2019; 129:105-117. [PMID: 31125730 DOI: 10.1016/j.envint.2019.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 05/21/2023]
Abstract
Understanding how microbial communities change with environmental degradation and restoration may offer new insights into the understudied ecology that connects humans, microbiota, and the natural world. Immunomodulatory microbial diversity and 'Old Friends' are thought to be supplemented from biodiverse natural environments, yet deficient in anthropogenically disturbed or degraded environments. However, few studies have compared the microbiomes of natural vs. human-altered environments and there is little knowledge of which microbial taxa are representative of ecological restoration-i.e. the assisted recovery of degraded ecosystems typically towards a more natural, biodiverse state. Here we use novel bootstrap-style resampling of site-level soil bacterial 16S rRNA gene environmental DNA data to identify genus-level indicators of restoration from a 10-year grassy eucalypt woodland restoration chronosequence at Mt Bold, South Australia. We found two key indicator groups emerged: 'opportunistic taxa' that decreased in relative abundance with restoration and more stable and specialist, 'niche-adapted taxa' that increased. We validated these results, finding seven of the top ten opportunists and eight of the top ten niche-adapted taxa displayed consistent differential abundance patterns between human-altered vs. natural samples elsewhere across Australia. Extending this, we propose a two-dimensional mapping for ecosystem condition based on the proportions of these divergent indicator groups. We also show that restoring a more biodiverse ecosystem at Mt Bold has increased the potentially immune-boosting environmental microbial diversity. Furthermore, environmental opportunists including the pathogen-containing genera Bacillus, Clostridium, Enterobacter, Legionella and Pseudomonas associated with disturbed ecosystems. Our approach is generalizable with potential to inform DNA-based methods for ecosystem assessment and help target environmental interventions that may promote microbiota-mediated human health gains.
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Affiliation(s)
- Craig Liddicoat
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
| | - Philip Weinstein
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Hobart, TAS, 7000, Australia.
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
| | - Michelle Waycott
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia.
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186
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de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. Front Microbiol 2019; 10:1680. [PMID: 31417506 PMCID: PMC6682628 DOI: 10.3389/fmicb.2019.01680] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.
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Affiliation(s)
- Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Raffaella Rossetto
- São Paulo's Agency for Agribusiness Technology APTA-SAA, Piracicaba, Brazil
| | - Robert Alan Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, United States
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Environmental Sciences, Federal University of São Carlos, Sorocaba, Brazil
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187
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Wei Z, Yu S, Huang Z, Xiao X, Tang M, Li B, Zhang X. Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:170-177. [PMID: 30927638 DOI: 10.1016/j.ecoenv.2019.03.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3- could be used as electron acceptor and Hg0 as electron donor in denitrification.
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Affiliation(s)
- Zaishan Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China.
| | - Shan Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Zaishan Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Xiaoliang Xiao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Meiru Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Bailong Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Xiao Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
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188
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Tian W, Wang H, Xiang X, Wang R, Xu Y. Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland. Front Microbiol 2019; 10:1661. [PMID: 31396183 PMCID: PMC6667737 DOI: 10.3389/fmicb.2019.01661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/04/2019] [Indexed: 11/13/2022] Open
Abstract
Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.
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Affiliation(s)
- Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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189
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Oyetibo GO, Miyauchi K, Huang Y, Ikeda-Ohtsubo W, Chien MF, Ilori MO, Amund OO, Endo G. Comparative geochemical evaluation of toxic metals pollution and bacterial communities of industrial effluent tributary and a receiving estuary in Nigeria. CHEMOSPHERE 2019; 227:638-646. [PMID: 31015084 DOI: 10.1016/j.chemosphere.2019.04.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/02/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Toxic metals/metalloid contaminations of estuarine sediments due to compromised tributaries arouse significant interest in studying bacterial community that triggers natural attenuation processes. Geo-accumulation index (Igeo), contamination factor (CF), pollution load index (PLI), and Hakanson potential ecological risk index (RI) as a sum of risk factors (Er) were used to quantify toxic metal/metalloid-pollution status of Lagos Lagoon (2W) and 'Iya-Alaro' tributary (4W) sediments in comparison with pristine 'Lekki Conservation Centre' sediment (L1-B). Bacteriology of the ecosystems was based on culture-independent analyses using pyrosequencing. 2W and 4W were extremely contaminated with mercury (Igeo > 7), whereas, cadmium contamination was only observed in 4W. The two ecosystems were polluted with toxic metal based on PLI, where mercury (Er = 2900 and 1900 for 4W and 2W, respectively) posed very high ecological risks. Molecular fingerprinting revealed that Proteobacteria, Firmicutes, and Acidobacteria predominately contributed the 20 most abundant genera in the two ecosystems. The 240 and 310 species present in 2W and 4W, respectively, but absent in L1-B, thrive under the metal concentrations in the polluted hydrosphere. Whereas, the 58,000 species missing in 2W and 4W but found in L1-B would serve as indicators for systems impacted with metal eco-toxicity. Despite toxic metal pollution of the ecosystems understudied, bacterial communities play vital roles in self-recovery processes occurring in the hydrosphere.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria; Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan.
| | - Keisuke Miyauchi
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Yi Huang
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan; Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Wakako Ikeda-Ohtsubo
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Mei-Fang Chien
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Matthew O Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - Ginro Endo
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
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190
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Schlatter DC, Reardon CL, Johnson-Maynard J, Brooks E, Kahl K, Norby J, Huggins D, Paulitz TC. Mining the Drilosphere: Bacterial Communities and Denitrifier Abundance in a No-Till Wheat Cropping System. Front Microbiol 2019; 10:1339. [PMID: 31316473 PMCID: PMC6611406 DOI: 10.3389/fmicb.2019.01339] [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: 02/02/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
Earthworms play important roles in no-till cropping systems by redistributing crop residue to lower soil horizons, providing macropores for root growth, increasing water infiltration, enhancing soil quality and organic matter, and stimulating nitrogen cycling. The soil impacted by earthworm activity, including burrows, casts, and middens, is termed the drilosphere. The objective of this study was to determine the effect of earthworms on soil microbial community composition in the drilosphere at different landscape slope positions. Soil cores (50 cm depth) were extracted from three landscape locations (top, middle, and bottom slope positions) on a sloping aspect of a no-till wheat farm. Soil was sampled at the bottom of the soil core from inside multiple earthworm (Lumbricus terrestris) channels (drilosphere) and from adjacent bulk soil. Bacterial communities were characterized for 16S rRNA gene diversity using high-throughput sequencing and functional denitrifier gene abundance (nirK, nirS, and nosZ) by quantitative PCR. Bacterial communities were structured primarily by the landscape slope position of the soil core followed by source (bulk versus drilosphere soil), with a significant interaction between core position and source. The families AKIW874, Chitinophagaceae, and Comamonadaceae and the genera Amycolatopsis, Caulobacter, Nocardioides, and Variovorax were more abundant in the drilosphere compared to the bulk soil. Most of the individual bacterial taxa enriched in the drilosphere versus bulk soil were members of Actinobacteria, including Micrococcales, Gaiellaceae, Solirubrobacterales, and Mycobacterium. In general, the greatest differences in communities were observed in comparisons of the top and bottom slope positions in which the bottom slope communities had significantly greater richness, diversity, and denitrifier abundance than the top slope position. Populations of denitrifiers (i.e., ratio of nirK+nirS to 16S rRNA) were more abundant in earthworm-impacted soils and there was a significant impact of L. terrestris on soil community composition which was observed only in the top landscape position. There were significant correlations between the abundance of nirK and nirS and taxa within Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, suggesting a broad diversity of denitrifying bacteria. Earthworms influence the soil microbial communities, but the impact depends on the slope location in a variable landscape, which likely reflects different soil characteristics.
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Affiliation(s)
- Daniel C. Schlatter
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States
| | - Catherine L. Reardon
- Soil and Water Conservation Research Unit, Agricultural Research Service, United States Department of Agriculture, Adams, OR, United States
| | - Jodi Johnson-Maynard
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, United States
| | - Erin Brooks
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, United States
| | - Kendall Kahl
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, United States
| | - Jessica Norby
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, United States
| | - David Huggins
- Northwest Sustainable Agroecosystems Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States
| | - Timothy C. Paulitz
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States
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191
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Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R. Establishing microbial composition measurement standards with reference frames. Nat Commun 2019; 10:2719. [PMID: 31222023 PMCID: PMC6586903 DOI: 10.1038/s41467-019-10656-5] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. Here, we demonstrate common pitfalls in comparing relative abundance across samples and identify two solutions that reveal microbial changes without the need to estimate total microbial load. We define the notion of "reference frames", which provide deep intuition about the compositional nature of microbiome data. In an oral time series experiment, reference frames alleviate false positives and produce consistent results on both raw and cell-count normalized data. Furthermore, reference frames identify consistent, differentially abundant microbes previously undetected in two independent published datasets from subjects with atopic dermatitis. These methods allow reassessment of published relative abundance data to reveal reproducible microbial changes from standard sequencing output without the need for new assays.
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Affiliation(s)
- James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Justin Silverman
- Program in Computational Biology and Bioinformatics, Duke University, Durham, 27708, USA
- Medical Scientist Training Program, Duke University, Durham, 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, 27708, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, 92037, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA.
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192
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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193
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Männistö M, Vuosku J, Stark S, Saravesi K, Suokas M, Markkola A, Martz F, Rautio P. Bacterial and fungal communities in boreal forest soil are insensitive to changes in snow cover conditions. FEMS Microbiol Ecol 2019; 94:5043222. [PMID: 29939247 DOI: 10.1093/femsec/fiy123] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
The northern regions are experiencing considerable changes in winter climate leading to more frequent warm periods, rain-on-snow events and reduced snow pack diminishing the insulation properties of snow cover and increasing soil frost and freeze-thaw cycles. In this study, we investigated how the lack of snow cover, formation of ice encasement and snow compaction affect the size, structure and activities of soil bacterial and fungal communities. Contrary to our hypotheses, snow manipulation treatments over one winter had limited influence on microbial community structure, bacterial or fungal copy numbers or enzyme activities. However, microbial community structure and activities shifted seasonally among soils sampled before snow melt, in early and late growing season and seemed driven by substrate availability. Bacterial and fungal communities were dominated by stress-resistant taxa such as the orders Acidobacteriales, Chaetothyriales and Helotiales that are likely adapted to adverse winter conditions. This study indicated that microbial communities in acidic northern boreal forest soil may be insensitive to direct effects of changing snow cover. However, in long term, the detrimental effects of increased ice and frost to plant roots may alter plant derived carbon and nutrient pools to the soil likely leading to stronger microbial responses.
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Affiliation(s)
- Minna Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Jaana Vuosku
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Sari Stark
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland.,Arctic Centre, University of Lapland, P.O. Box 122, FI-96101 Rovaniemi, Finland
| | - Karita Saravesi
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Marko Suokas
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Annamari Markkola
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Françoise Martz
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Pasi Rautio
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
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194
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Beule L, Chen KH, Hsu CM, Mackowiak C, Dubeux Jr. JC, Blount A, Liao HL. Soil bacterial and fungal communities of six bahiagrass cultivars. PeerJ 2019; 7:e7014. [PMID: 31179193 PMCID: PMC6545100 DOI: 10.7717/peerj.7014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/19/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. OBJECTIVES This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. METHODS Six bahiagrass cultivars ('Argentine', 'Pensacola', 'Sand Mountain', 'Tifton 9', 'TifQuik', and 'UF-Riata') were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. RESULTS The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under 'Sand Mountain' than 'UF-Riata'. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. CONCLUSIONS Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.
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Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Georg-August Universität Göttingen, Goettingen, Germany
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Ko-Hsuan Chen
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Chih-Ming Hsu
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Jose C.B. Dubeux Jr.
- North Florida Research and Education Center, University of Florida, Marianna, FL, United States of America
| | - Ann Blount
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
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195
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Li Z, Qiu K, Schneider RL, Morreale SJ, Xie Y. Comparison of microbial community structures in soils with woody organic amendments and soils with traditional local organic amendments in Ningxia of Northern China. PeerJ 2019; 7:e6854. [PMID: 31119077 PMCID: PMC6511227 DOI: 10.7717/peerj.6854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023] Open
Abstract
Background Addition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood. Methods Three locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla. Results Both bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment. Conclusion New local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with CS, but different from the most traditional local organic amendment with CM in Ningxia, Northern China. Moreover, the high C/N-sensitive, and lignin and cellulose decompose-related microbial phyla increased in CS and PB have benefits in decomposing those incorporated organic materials and improving soil properties. Therefore, we recommend that PB should also be considered as a viable soil organic amendment for future not in Ningxia, but also in other places.
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Affiliation(s)
- Zhigang Li
- School of Agriculture, Ningxia University, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, Ningxia, China
| | - Rebecca L Schneider
- Department of Nature Resources, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Stephen J Morreale
- Department of Nature Resources, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, Ningxia, China
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196
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Barba C, Folch A, Sanchez-Vila X, Martínez-Alonso M, Gaju N. Are dominant microbial sub-surface communities affected by water quality and soil characteristics? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:332-343. [PMID: 30818236 DOI: 10.1016/j.jenvman.2019.02.079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO3 and SO4, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.
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Affiliation(s)
- Carme Barba
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Albert Folch
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Xavier Sanchez-Vila
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), C/Jordi Girona 1-3, 08034, Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain.
| | - Maira Martínez-Alonso
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
| | - Núria Gaju
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
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197
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Neher DA, Cutler AJ, Weicht TR, Sharma M, Millner PD. Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach. J Appl Microbiol 2019; 126:1910-1922. [PMID: 30925006 DOI: 10.1111/jam.14268] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/01/2019] [Accepted: 03/25/2019] [Indexed: 11/26/2022]
Abstract
AIMS The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources. METHOD AND RESULTS Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH4 -N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful. CONCLUSIONS Dairy-based composts are less likely to support E. coli survival than poultry-based composts. SIGNIFICANCE AND IMPACT OF THE STUDY Results aid in risk assessment of the use of different types of manure-based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.
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Affiliation(s)
- D A Neher
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - A J Cutler
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - T R Weicht
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - M Sharma
- Environmental Microbial and Food Safety Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville, MD, USA
| | - P D Millner
- Environmental Microbial and Food Safety Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville, MD, USA
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198
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Lacerda-Júnior GV, Noronha MF, Cabral L, Delforno TP, de Sousa STP, Fernandes-Júnior PI, Melo IS, Oliveira VM. Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest. Front Microbiol 2019; 10:648. [PMID: 31024471 PMCID: PMC6461016 DOI: 10.3389/fmicb.2019.00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 12/21/2022] Open
Abstract
Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.
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Affiliation(s)
- Gileno V. Lacerda-Júnior
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Melline F. Noronha
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Lucélia Cabral
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Tiago P. Delforno
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Sanderson Tarciso Pereira de Sousa
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | | | - Itamar S. Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Valéria M. Oliveira
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
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He Z, Mao R, Dong JE, Liang Z, Zhang H, Liu L. Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation. Can J Microbiol 2019; 65:282-295. [DOI: 10.1139/cjm-2018-0409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pinellia ternata is a traditional Chinese herb that suffers from continuous cropping (CC), which significantly decreases both yield and quality. The influence of CC on the microbiome in P. ternata rhizosphere and the effects of remediation on microbiota by rotational cropping (CR) were assessed by Illumina high-throughput sequencing technology. CC tends to decrease the α-diversities as a function of cultivation time, whereas CR tends to increase them. Differentially abundant analysis showed that microbial structure was important in maintaining the health status of P. ternata rhizosphere. Results suggested that CC soils were mainly enriched for Pseudomonas, Rhizobium, and Streptophyta operational taxonomic units (OTUs), while the CR soils were mainly enriched for Rhizobium, Pseudomonas, Flavobacterium, Sphingomonas, Rhizobacter, and Arthrobacter OTUs. On the basis of the community dissimilarities, we grouped all sample replicates into three post hoc clusters in which soils were defined as healthy, health-suppressed, and health-depressed soils. The three soil types represented different soil physicochemical properties. The activities of the microbiome features, including ammonia oxidizer, sulfate reducer, nitrite reducer, dehalogenation, xylan degrader, sulfide oxidizer, nitrogen fixation, atrazine metabolism, chitin degradation, degraded aromatic hydrocarbons, and chlorophenol degradation, were also considerably different among the three soils.
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Affiliation(s)
- Zhigui He
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- Institute of Food Science and Biological Engineering, Guilin Tourism University, Guilin 541006, P.R. China
| | - Renjun Mao
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Juan e Dong
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Haihua Zhang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Lin Liu
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
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200
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Lu J, Yang Z, Xu W, Shi X, Guo R. Enrichment of thermophilic and mesophilic microbial consortia for efficient degradation of corn stalk. J Environ Sci (China) 2019; 78:118-126. [PMID: 30665630 DOI: 10.1016/j.jes.2018.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 06/09/2023]
Abstract
Six different environmental samples were applied to enrich microbial consortia for efficient degradation of corn stalk, under the thermophilic and mesophilic conditions. The consortium obtained from anaerobic digested sludge under thermophilic condition (TC-Y) had the highest lignocellulose-degrading activity. The CO2 yield was 246.73 mL/g VS in 23 days, meanwhile, the maximum CO2 production rate was 15.48 mL/(CO2·d), which was 28.75% and 52.27% higher than that under mesophilic condition, respectively. The peak value of cellulase activity reached 0.105 U/mL, which was at least 34.61% higher than the other groups. In addition, 49.5% of corn stalk was degraded in 20 days, moreover, the degradation ratio of cellulose, hemicellulose and lignin can reach 52.76%, 62.45% and 42.23%, respectively. Microbial consortium structure analysis indicated that the TC-Y contained the phylum of Gemmatimonadetes, Acidobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Proteobacteria. Furthermore, the Pseudoxanthomonas belonging to GammaProteobacteria might be the key bacterial group for the lignocellulose degradation. These results indicated the capability of degrading un-pretreated corn stalk and the potential for further investigation and application of TC-Y.
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Affiliation(s)
- Jun Lu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China. E-mail: (Jun Lu), (Zhiman Yang); University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiman Yang
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China. E-mail: (Jun Lu), (Zhiman Yang)
| | - Wanying Xu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China. E-mail: (Jun Lu), (Zhiman Yang)
| | - Xiaoshuang Shi
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China. E-mail: (Jun Lu), (Zhiman Yang)
| | - Rongbo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China. E-mail: (Jun Lu), (Zhiman Yang).
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