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Johnson J, Jain KR, Patel A, Parmar N, Joshi C, Madamwar D. Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal. World J Microbiol Biotechnol 2023; 40:52. [PMID: 38146029 DOI: 10.1007/s11274-023-03848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023]
Abstract
Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.
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Affiliation(s)
- Jenny Johnson
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Kunal R Jain
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Anand Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Nidhi Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, 6th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa (Anand), Gujarat, 388 421, India.
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2
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Yan B, Jiang L, Zhou H, Okokon Atakpa E, Bo K, Li P, Xie Q, Li Y, Zhang C. Performance and microbial community analysis of combined bioreactors in treating high-salinity hydraulic fracturing flowback and produced water. BIORESOURCE TECHNOLOGY 2023; 386:129469. [PMID: 37451509 DOI: 10.1016/j.biortech.2023.129469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The anoxic/oxic systems are a widely used biological strategy for wastewater treatment. However, little is known about the performance and microbial community correlation of different combined bioreactors in the treatment of high-COD and high-salinity hydraulic fracturing flowback and produced water (HF-FPW). In this study, the performance of Up-flow anaerobic sludge bed-bio-contact oxidation reactor (UASB-BCOR) and Fixed-bed baffled reactor (FBR-BCOR) in treating HF-FPW was investigated and compared. The results suggested the FBR-BCOR could efficiently remove COD, SS, NH4+-N, and oil pollutants, and it exhibited better resistance to the negative interference of hydraulic shock load on it. Besides, the correlation analysis first disclosed the key functional genera during the degradation process, including Ignavibacterium, Ellin6067, and Zixibacteria. Moreover, network analysis revealed that the difference of microbial co-occurrence network structure is the main driving factor for the difference of bioreactor processing capacity. This work demonstrates the feasibility and potential of FBR-BCOR in treating HF-FPW.
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Affiliation(s)
- Bozhi Yan
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Lijia Jiang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Hanghai Zhou
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Edidiong Okokon Atakpa
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Kuiyong Bo
- Xinjiang Keli New Technology Development Co., Ltd., Karamay 834000, Xinjiang, China
| | - Pingyuan Li
- Xinjiang Keli New Technology Development Co., Ltd., Karamay 834000, Xinjiang, China
| | - Qinglin Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Yanhong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Chunfang Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China.
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3
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Zaitseva S, Badmaev N, Kozyreva L, Dambaev V, Barkhutova D. Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia). Microorganisms 2022; 10:2202. [PMID: 36363794 PMCID: PMC9695985 DOI: 10.3390/microorganisms10112202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2023] Open
Abstract
Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.
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Affiliation(s)
- Svetlana Zaitseva
- Institute of General and Experimental Biology SD RAS, 670047 Ulan-Ude, Russia
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Proposal of a New Method for Controlling the Thaw of Permafrost around the China–Russia Crude Oil Pipeline and a Preliminary Study of Its Ventilation Capacity. WATER 2021. [DOI: 10.3390/w13202908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The China–Russia crude oil pipeline (CRCOP) has been in operation for over ten years. Field observation results have shown that a thaw bulb has developed around the CRCOP which expands at a rate of more than 0.8 m∙a−1 in depth. In view of the deficits of existing measures in mitigating permafrost thaw, a new control method is proposed based on active cooling. According to the relationship between total pressure loss and the driving force of natural ventilation, the wind speed in a U-shaped air-ventilation pipe around the CRCOP is calculated. By analyzing the theoretical calculation and numerical analysis results, it is found that the influence of thermal pressure difference on the natural ventilation of the structure can be negligible, and the influences of resistance loss along the pipe and local resistance loss in the pipe are similarly negligible. Exhaust elbows greatly improve the ventilation performance of the U-shaped air-ventilated pipe. This study developed a novel structure around warm-oil pipelines in permafrost for mitigating thaw settlement along the CRCOP and other similar projects across the world.
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Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil. 3 Biotech 2020; 10:42. [PMID: 31988836 DOI: 10.1007/s13205-019-2027-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
This study investigated the impacts of crude oil, diesel, and gasoline on the diversity of indigenous microbial communities as well as culturable microorganisms in the studied soil. Oil contamination led to shifts in the diversity of the soil's microbial communities, regardless of the contaminant applied. Unpolluted soils were more diverse and evenly distributed than contaminated samples. The domain Bacteria accounted for 65.15% of the whole microbial community. The bacterial phylum Proteobacteria dominated in all samples, followed by Actinobacteria and Acidobacteria. Pseudomonas with 28.15% of reads dominated in Proteobacteria, while Rhodococcus (3.07%) dominated in Actinobacteria, and Blastocatella (2.53%) dominated in Acidobacteria. The dominant fungal phyla across all samples were Ascomycota dominated by Penicillium (50.48% of sequences), and Zygomycota dominated by Mortierella (16.87%). Sequences similar to the archaeal phyla, Euryarchaeota and Thaumarchaeota, were also detected. The number of culturable microorganisms increased following the contamination and was higher in contaminated samples than in clean samples. Oil contamination also resulted in the enrichment of oil-degrading strains. Two bacteria, Serratia marcescens strain PL and Raoultella ornithinolytica PS, which were isolated from crude oil-contaminated soil, exhibited strong crude oil degradation ability. Strain PL was the most efficient strain and degraded 75.10% of crude oil, while strain PL degraded 65.48%, after 20 days of incubation. However, the mixed culture of the two strains was more effective than single strain and could achieve up to 96.83% of crude oil degradation, with a complete abatement of straight-chain hydrocarbons (from C12 to C25), and more than 91% removal of highly branched hydrocarbons, phytane and pristane, which are known to be more recalcitrant to biodegradation. Strains PS and PL are two newly isolated crude oil degraders that are not among the most prominent crude oil-degrading strains referenced in the literature. Therefore, their high degradation capacity makes them perfect candidates for the bioremediation of petroleum hydrocarbon contaminated environments.
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Farber R, Rosenberg A, Rozenfeld S, Banet G, Cahan R. Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste. Microorganisms 2019; 7:E497. [PMID: 31661854 PMCID: PMC6921085 DOI: 10.3390/microorganisms7110497] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/19/2019] [Accepted: 10/26/2019] [Indexed: 11/16/2022] Open
Abstract
Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day-1 and 7.8 mg day-1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day-1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.
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Affiliation(s)
- Ravit Farber
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Alona Rosenberg
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Shmuel Rozenfeld
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Gabi Banet
- Dead Sea-Arava Science Center, Arava 86910, Israel.
| | - Rivka Cahan
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
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Rakitin A, Beletsky A, Mardanov A, Surgucheva N, Sorokin V, Cherbunina M, Brouchkov A, Mulyukin A, Filippova S. Prokaryotic community in Pleistocene ice wedges of Mammoth Mountain. Extremophiles 2019; 24:93-105. [PMID: 31606813 DOI: 10.1007/s00792-019-01138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/30/2019] [Indexed: 01/21/2023]
Abstract
Ice wedges differ from other types of surface and underground glacial bodies and are widely spread in perennially frozen sub-Arctic regions, but the bacterial and archaeal diversity in these permafrost features remains poorly studied. Here, we compared the prokaryotic community composition in the active layer and ancient, 13-19 kyr BP and ~ 40 kyr BP, ice wedge horizons from the same exposure profile of the Mammoth Mountain, using pyrosequencing 16S rRNA gene. The most abundant OTUs in the active layer were affiliated with Acidobacteria (31.81%) followed by Actinobacteria (18.29%), Proteobacteria (18.14%), Gemmatimonadetes (7.3%), Parcubacteria (7.13%) and Bacteroidetes (6.49%). The prokaryotic community in 13-19 kyr BP ice wedge differed at the phylum level by the predominance of Actinobacteria (29.15%) over Acidobacteria (19.52%), Proteobacteria (18.45%), Verrumicrobia (5.88%), Firmicutes (2.98%) and Gemmatimonadetes (2.87%). In contrast, the oldest (~ 40 kyr BP) ice wedge prokaryotic community was rather poor, and only three phyla Firmicutes (54.48%), Proteobacteria (31.42%) and Bacteroidetes (7.92%) constituted the major fraction of reads. Archaeal sequences contributed with no more than 0.6% to total reads in all studied samples. Apparently, the Mammoth Mountain exposure profile harbors insular microbial communities with specific structure that reflects the stratigraphy, properties and age.
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Affiliation(s)
- Andrey Rakitin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia.
| | - Aleksey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Natalya Surgucheva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | | | - Anatoli Brouchkov
- Moscow State University, Leninskiye Gory 1, Moscow, 11999, Russia.,Tyumen State University, Volodarskogo St. 6, Tyumen, 625003, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Svetlana Filippova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
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Zhang J, Chen M, Huang J, Guo X, Zhang Y, Liu D, Wu R, He H, Wang J. Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea. PLoS One 2019; 14:e0215328. [PMID: 30973915 PMCID: PMC6459509 DOI: 10.1371/journal.pone.0215328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023] Open
Abstract
The nitrogen (N) cycle is closely related to the stability of marine ecosystems. Microbial communities have been directly linked to marine N-cycling processes. However, systematic research on the bacterial community composition and diversity involved in N cycles in different seas is lacking. In this study, microbial diversity in the Bohai Sea (BHS), Yellow Sea (YS) and South China Sea (SCS) was surveyed by targeting the hypervariable V4 regions of the 16S rRNA gene using next-generation sequencing (NGS) technology. A total of 2,505,721 clean reads and 15,307 operational taxonomic units (OTUs) were obtained from 86 sediment samples from the three studied China seas. LEfSe analysis demonstrated that the SCS had more abundant microbial taxa than the BHS and YS. Diversity indices demonstrated that Proteobacteria and Planctomycetes were the dominant phyla in all three China seas. Canonical correspondence analysis (CCA) indicated that pH (P = 0.034) was the principal determining factors, while the organic matter content, depth and temperature had a minor correlated with the variations in sedimentary microbial community distribution. Cluster and functional analyses of microbial communities showed that chemoheterotrophic and aerobic chemoheterotrophic microorganisms widely exist in these three seas. Further research found that the cultivable protease-producing bacteria were mainly affiliated with the phyla Proteobacteria, Firmicutes and Bacteroidetes. It was very clear that Pseudoalteromonadaceae possessed the highest relative abundance in the three sea areas. The predominant protease-producing genera were Pseudoalteromonas and Bacillus. These results shed light on the differences in bacterial community composition, especially protease-producing bacteria, in these three China seas.
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Affiliation(s)
- Jiang Zhang
- School of Life Science, Central South University, Changsha, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, China
| | - Jiafeng Huang
- School of Life Science, Central South University, Changsha, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, China
| | - Yanjiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Dan Liu
- School of Life Science, Central South University, Changsha, China
| | - Ribang Wu
- School of Life Science, Central South University, Changsha, China
| | - Hailun He
- School of Life Science, Central South University, Changsha, China
- * E-mail: (HH); (GW)
| | - Jun Wang
- School of Life Science, Central South University, Changsha, China
- Sanway Gene Technology Inc., Changsha, China
- * E-mail: (HH); (GW)
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Ding Y, Wei J, Xiong J, Zhou B, Cai H, Zhu W, Zhang H. Effects of operating parameters on in situ NH 3 emission control during kitchen waste composting and correlation analysis of the related microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:11756-11766. [PMID: 30815814 DOI: 10.1007/s11356-019-04605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Ammonia emission during composting results in anthropogenic odor nuisance and reduces the agronomic value of the compost due to the loss of nitrogen. Adjusting the operating parameters during composting is an emerging in situ odor control technique that is cheap and highly efficient. The effects of in situ NH3 emission control were investigated in this study by simultaneously adjusting key operating parameters (such as C/N ratio, aeration rate, and moisture content) during the composting processes (C1-C9). Results showed that the average NH3 emission concentrations for different treatments were in the order of C1 > C4 > C2 > C5 > C3 > C6 > C7 > C8 > C9. The total content of NH3 emission (21.02 g/kg) in C9 (C/N ratio = 35, aeration rate = 15 L/min, and moisture content = 60%) was much lower than that (65.95 g/kg) in C1 (C/N ratio = 15, aeration rate = 5 L/min, and moisture content = 60%). The nitrogen loss ratio was 27.36% for C1, while 16.15% for C9. The microbial diversity and abundance in C9 and C1 were compared using high-throughput sequencing. The relationship between NH3 emission, operating parameters, and the related functional microbial communities was also investigated. Results revealed that Nitrosospira, Nitrosomonas, Nitrobacter, Pseudomonas, Methanosaeta, Rhodobacter, Paracoccus, and Sphingobacterium were negatively related to NH3 emission. According to the above results, the optimal values for different operating parameters for the in situ NH3 control during kitchen waste composting were, respectively, moisture content of 70%, C/N ratio of 35, and aeration rate of 15 L/min, with the order of effectiveness from high to low being aeration rate > C/N > moisture. This information could be used as a valuable reference for the in situ NH3 emission control during kitchen waste composting.
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Affiliation(s)
- Ying Ding
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China.
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China.
| | - Jiaojiao Wei
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
| | - Junsheng Xiong
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
| | - Bowei Zhou
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
| | - Hanjiang Cai
- China National Bamboo Research Center, Hangzhou, 310012, People's Republic of China
| | - Weiqin Zhu
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
| | - Hangjun Zhang
- Department of Environmental Engineering, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
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Khudur LS, Gleeson DB, Ryan MH, Shahsavari E, Haleyur N, Nugegoda D, Ball AS. Implications of co-contamination with aged heavy metals and total petroleum hydrocarbons on natural attenuation and ecotoxicity in Australian soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:94-102. [PMID: 30172128 DOI: 10.1016/j.envpol.2018.08.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/27/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
The bioremediation of historic industrial contaminated sites is a complex process. Co-contamination, often with lead which was commonly added to gasoline until 16 years ago is one of the biggest challenges affecting the clean-up of these sites. In this study, the effect of heavy metals, as co-contaminant, together with total petroleum hydrocarbons (TPH) is reported, in terms of remaining soil toxicity and the structure of the microbial communities. Contaminated soil samples from a relatively hot and dry climate in Western Australia were collected (n = 27). Analysis of soils showed the presence of both contaminants, TPHs and heavy metals. The Microtox test confirmed that their co-presence elevated the remaining ecotoxicity. Toxicity was correlated with the presence of lead, zinc and TPH (0.893, 0.599 and 0.488), respectively, assessed using Pearson Correlation coefficient factor. Next Generation Sequencing of soil bacterial 16S rRNA, revealed a lack of dominate genera; however, despite the variation in soil type, a few genera including Azospirillum spp. and Conexibacter were present in most soil samples (85% and 82% of all soils, respectively). Likewise, many genera of hydrocarbon-degrading bacteria were identified in all soil samples. Streptomyces spp. was presented in 93% of the samples with abundance between 7% and 40%. In contrast, Acinetobacter spp. was found in only one sample but was a dominant member of (45%) of the microbial community. In addition, some bacterial genera were correlated to the presence of the heavy metals, such as Geodermatophilus spp., Rhodovibrio spp. and Rubrobacter spp. which were correlated with copper, lead and zinc, respectively. This study concludes that TPH and heavy metal co-contamination significantly elevated the associated toxicity. This is an important consideration when carrying out risk assessment associated with natural attenuation. This study also improves knowledge about the dynamics of microbial communities in mixed contamination scenarios.
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Affiliation(s)
- Leadin S Khudur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia.
| | - Deirdre B Gleeson
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Megan H Ryan
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Nagalakshmi Haleyur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Dayanthi Nugegoda
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
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11
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Spini G, Spina F, Poli A, Blieux AL, Regnier T, Gramellini C, Varese GC, Puglisi E. Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi. Front Microbiol 2018; 9:2543. [PMID: 30425689 PMCID: PMC6218658 DOI: 10.3389/fmicb.2018.02543] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
Abstract
Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.
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Affiliation(s)
- Giulia Spini
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Federica Spina
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | | | | | | | - Giovanna C. Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
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12
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Müller O, Bang-Andreasen T, White RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol 2018; 20:4328-4342. [PMID: 29971895 DOI: 10.1111/1462-2920.14348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.
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Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway
| | - Toke Bang-Andreasen
- Department of Environmental Science, Aarhus University, DK-4000, Roskilde, Denmark.,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
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13
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Kotoky R, Rajkumari J, Pandey P. The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:858-870. [PMID: 29660711 DOI: 10.1016/j.jenvman.2018.04.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.
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Affiliation(s)
- Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, 788011, India.
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14
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Ren B, Hu Y, Chen B, Zhang Y, Thiele J, Shi R, Liu M, Bu R. Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China. Sci Rep 2018; 8:5619. [PMID: 29618759 PMCID: PMC5884794 DOI: 10.1038/s41598-018-24040-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/26/2018] [Indexed: 12/21/2022] Open
Abstract
In the permafrost region of northeastern China, vegetation and soil environment have showed response to permafrost degradation triggered by global warming, but the corresponding variation of the soil microbial communities remains poorly investigated. Here, a field investigation in the continuous permafrost region was conducted to collect 63 soil samples from 21 sites along a latitudinal gradient to assess the distribution pattern of microbial communities and their correlation with environmental factors. High-throughput Illumina sequencing revealed that bacterial communities were dominated by Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria. Both microbial richness and phylogenetic diversity decreased initially and then increased as the latitude increased. UniFrac analysis of microbial communities detected significant differences among latitudes. Variation partitioning analysis and structural equation models revealed that environmental variables, including geographic factors, plant-community factors and soil physicochemical factors, all played non-negligible roles in affecting the microbial community structures directly or indirectly. Redundancy analysis and boosted regression tree analysis further highlighted the influences of soil pH and plant richness on microbial community compositions and diversity patterns. Taken together, these results suggest that the distribution pattern of soil microbial communities shows distinct changes along the latitudinal gradients in northeastern China and is predominantly mediated by soil pH and plant diversity.
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Affiliation(s)
- Baihui Ren
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Yuanman Hu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Baodong Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Zhang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Jan Thiele
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Rongjiu Shi
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Miao Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Rencang Bu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.
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15
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Berlanga M, Palau M, Guerrero R. Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats. Front Microbiol 2017; 8:2619. [PMID: 29312277 PMCID: PMC5744480 DOI: 10.3389/fmicb.2017.02619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.
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Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona - Institut d'Investigació Biomédica de Bellvitge, Barcelona, Spain.,Academia Europaea-Barcelona Knowledge Hub, Barcelona, Spain
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16
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Brouchkov A, Kabilov M, Filippova S, Baturina O, Rogov V, Galchenko V, Mulyukin A, Fursova O, Pogorelko G. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia). Gene 2017; 636:48-53. [PMID: 28916375 DOI: 10.1016/j.gene.2017.09.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 09/30/2022]
Abstract
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species.
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Affiliation(s)
- Anatoli Brouchkov
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Tyumen State University, Volodarskogo 6, Tyumen 625003, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Svetlana Filippova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Victor Rogov
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Valery Galchenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Oksana Fursova
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Gennady Pogorelko
- NI Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
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17
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Idris H, Goodfellow M, Sanderson R, Asenjo JA, Bull AT. Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert. Sci Rep 2017; 7:8373. [PMID: 28827739 PMCID: PMC5566421 DOI: 10.1038/s41598-017-08937-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/04/2017] [Indexed: 11/23/2022] Open
Abstract
The Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial 'dark matter', evidenced by a detected increase of 34% in families against those that are validly published. Rank-abundance analyses indicated that these soils were high-diversity habitats and that the great majority of designated 'rare' genera (up to 60% of all phylotypes) were always rare. These studies have enabled a core actinobacterial microbiome common to both habitats to be defined. The great majority of detected taxa have not been recovered by culture dependent methods, neither, with very few exceptions, has their functional ecology been explored. A microbial seed bank of this magnitude has significance not just for Atacama soil ecosystem resilience but represents an enormous untapped resource for biotechnology discovery programmes in an era where resistance to existing antibiotics is rapidly becoming a major threat to global health.
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Affiliation(s)
- Hamidah Idris
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
| | - Michael Goodfellow
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
| | - Roy Sanderson
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Alan T. Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ Kent, United Kingdom
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18
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The performance and microbial communities of biodegradation-electron transfer with sulfur metabolism integrated process for flue gas desulfurization wastewater treatment. Bioprocess Biosyst Eng 2017; 40:1543-1553. [DOI: 10.1007/s00449-017-1810-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/29/2017] [Indexed: 11/25/2022]
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19
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Thijs S, Op De Beeck M, Beckers B, Truyens S, Stevens V, Van Hamme JD, Weyens N, Vangronsveld J. Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys. Front Microbiol 2017; 8:494. [PMID: 28400755 PMCID: PMC5368227 DOI: 10.3389/fmicb.2017.00494] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies.
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Affiliation(s)
- Sofie Thijs
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | | | - Bram Beckers
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Sascha Truyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Vincent Stevens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University Kamloops, BC, Canada
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
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20
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Salam LB, Obayori SO, Nwaokorie FO, Suleiman A, Mustapha R. Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:7139-7159. [PMID: 28093673 DOI: 10.1007/s11356-017-8364-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.
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Affiliation(s)
- Lateef B Salam
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria.
| | - Sunday O Obayori
- Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria
| | - Francisca O Nwaokorie
- Department of Medical Laboratory Science, College of Medicine, University of Lagos, Akoka, Lagos, Nigeria
| | - Aisha Suleiman
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
| | - Raheemat Mustapha
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
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21
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Yang S, Wen X, Shi Y, Liebner S, Jin H, Perfumo A. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments. Sci Rep 2016; 6:37473. [PMID: 27886221 PMCID: PMC5122841 DOI: 10.1038/srep37473] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023] Open
Abstract
Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.
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Affiliation(s)
- Sizhong Yang
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Xi Wen
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.,College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Yulan Shi
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Huijun Jin
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, China
| | - Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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22
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He T, Zhang X. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:232-241. [PMID: 26626941 DOI: 10.1007/s10126-015-9683-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.
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Affiliation(s)
- Tianliang He
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Patel V, Sharma A, Lal R, Al-Dhabi NA, Madamwar D. Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates. BMC Microbiol 2016; 16:50. [PMID: 27001503 PMCID: PMC4802719 DOI: 10.1186/s12866-016-0669-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/09/2016] [Indexed: 01/27/2023] Open
Abstract
Background Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Results Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum “Proteobacteria” and genus “Chromobacterium,” respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. Conclusion To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0669-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vrutika Patel
- Post Graduate Department of Biosciences, Centre of Advanced Study in Bioresource Technology, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Gujarat, India
| | | | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriya Chair for Environmental Studies, College of Science, King Saud University, P.O. Box # 2455, Riyadh, 11451, Saudi Arabia
| | - Datta Madamwar
- Post Graduate Department of Biosciences, Centre of Advanced Study in Bioresource Technology, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Gujarat, India.
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Thijs S, Sillen W, Rineau F, Weyens N, Vangronsveld J. Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism. Front Microbiol 2016; 7:341. [PMID: 27014254 PMCID: PMC4792885 DOI: 10.3389/fmicb.2016.00341] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/03/2016] [Indexed: 11/23/2022] Open
Abstract
Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.
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Affiliation(s)
- Sofie Thijs
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | | | | | | | - Jaco Vangronsveld
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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Fuentes S, Barra B, Caporaso JG, Seeger M. From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation. Appl Environ Microbiol 2016; 82:888-96. [PMID: 26590285 PMCID: PMC4725283 DOI: 10.1128/aem.02625-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 11/16/2015] [Indexed: 02/02/2023] Open
Abstract
Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.
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Affiliation(s)
- Sebastián Fuentes
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center of Nanotechnology and Systems Biology, Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Bárbara Barra
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center of Nanotechnology and Systems Biology, Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center of Nanotechnology and Systems Biology, Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol 2016; 92:fiw018. [DOI: 10.1093/femsec/fiw018] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 01/08/2023] Open
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Hu W, Zhang Q, Tian T, Li D, Cheng G, Mu J, Wu Q, Niu F, Stegen JC, An L, Feng H. Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China. PLoS One 2015; 10:e0145747. [PMID: 26699734 PMCID: PMC4689587 DOI: 10.1371/journal.pone.0145747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/08/2015] [Indexed: 11/19/2022] Open
Abstract
Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent permafrost thaw.
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Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qi Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tian Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dingyao Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Gang Cheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jing Mu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qingbai Wu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, China
| | - Fujun Niu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, China
| | - James C. Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States of America
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huyuan Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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Stella T, Covino S, Burianová E, Filipová A, Křesinová Z, Voříšková J, Větrovský T, Baldrian P, Cajthaml T. Chemical and microbiological characterization of an aged PCB-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 533:177-186. [PMID: 26156136 DOI: 10.1016/j.scitotenv.2015.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
This study was aimed at complex characterization of three soil samples (bulk soil, topsoil and rhizosphere soil) from a site historically contaminated with polychlorinated biphenyls (PCB). The bulk soil was the most highly contaminated, with a PCB concentration of 705.95 mg kg(-1), while the rhizosphere soil was the least contaminated (169.36 mg kg(-1)). PCB degradation intermediates, namely chlorobenzoic acids (CBAs), were detected in all the soil samples, suggesting the occurrence of microbial transformation processes over time. The higher content of organic carbon in the topsoil and rhizosphere soil than in the bulk soil could be linked to the reduced bioaccessibility (bioavailability) of these chlorinated pollutants. However, different proportions of the PCB congener contents and different bioaccessibility of the PCB homologues indicate microbial biotransformation of the compounds. The higher content of organic carbon probably also promoted the growth of microorganisms, as revealed by phospholipid fatty acid (PFLA) quantification. Tag-encoded pyrosequencing analysis showed that the bacterial community structure was significantly similar among the three soils and was predominated by Proteobacteria (44-48%) in all cases. Moreover, analysis at lower taxonomic levels pointed to the presence of genera (Sphingomonas, Bulkholderia, Arthrobacter, Bacillus) including members with reported PCB removal abilities. The fungal community was mostly represented by Basidiomycota and Ascomycota, which accounted for >80% of all the sequences detected in the three soils. Fungal taxa with biodegradation potential (Paxillus, Cryptococcus, Phoma, Mortierella) were also found. These results highlight the potential of the indigenous consortia present at the site as a starting point for PCB bioremediation processes.
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Affiliation(s)
- T Stella
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy; Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - S Covino
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - E Burianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - A Filipová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Z Křesinová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - J Voříšková
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - T Větrovský
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - P Baldrian
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - T Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague 2, Czech Republic.
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A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities. Indian J Microbiol 2015; 55:406-14. [PMID: 26543266 DOI: 10.1007/s12088-015-0551-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022] Open
Abstract
The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.
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Wei C, He W, Wei L, Li C, Ma J. The Analysis of a Microbial Community in the UV/O3-Anaerobic/Aerobic Integrated Process for Petrochemical Nanofiltration Concentrate (NFC) Treatment by 454-Pyrosequencing. PLoS One 2015; 10:e0139991. [PMID: 26461260 PMCID: PMC4603877 DOI: 10.1371/journal.pone.0139991] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/21/2015] [Indexed: 01/24/2023] Open
Abstract
In this study, high-throughput pyrosequencing was applied on the analysis of the microbial community of activated sludge and biofilm in a lab-scale UV/O3- anaerobic/aerobic (A/O) integrated process for the treatment of petrochemical nanofiltration concentrate (NFC) wastewater. NFC is a type of saline wastewater with low biodegradability. From the anaerobic activated sludge (Sample A) and aerobic biofilm (Sample O), 59,748 and 51,231 valid sequence reads were obtained, respectively. The dominant phylotypes related to the metabolism of organic compounds, polycyclic aromatic hydrocarbon (PAH) biodegradation, assimilation of carbon from benzene, and the biodegradation of nitrogenous organic compounds were detected as genus Clostridium, genera Pseudomonas and Stenotrophomonas, class Betaproteobacteria, and genus Hyphomicrobium. Furthermore, the nitrite-oxidising bacteria Nitrospira, nitrite-reducing and sulphate-oxidising bacteria (NR-SRB) Thioalkalivibrio were also detected. In the last twenty operational days, the total Chemical Oxygen Demand (COD) and Total Organic Carbon (TOC) removal efficiencies on average were 64.93% and 62.06%, respectively. The removal efficiencies of ammonia nitrogen and Total Nitrogen (TN) on average were 90.51% and 75.11% during the entire treatment process.
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Affiliation(s)
- Chao Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
| | - Wenjie He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
- Tianjin Waterworks Group Co., Ltd., Tianjin, People's Republic of China
| | - Li Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
- * E-mail:
| | - Chunying Li
- School of Energy and Civil Engineering, Harbin University of Commerce, Harbin, Heilongjiang, People's Republic of China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang, People's Republic of China
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Hu W, Zhang Q, Tian T, Cheng G, An L, Feng H. The microbial diversity, distribution, and ecology of permafrost in China: a review. Extremophiles 2015; 19:693-705. [PMID: 25925876 DOI: 10.1007/s00792-015-0749-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/04/2015] [Indexed: 11/29/2022]
Abstract
Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.
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Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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Abed RMM, Al-Kindi S, Al-Kharusi S. Diversity of bacterial communities along a petroleum contamination gradient in desert soils. MICROBIAL ECOLOGY 2015; 69:95-105. [PMID: 25103912 DOI: 10.1007/s00248-014-0475-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box: 36, 123 Al Khoud, Muscat, Sultanate of Oman,
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Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Čapek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol 2014; 5:541. [PMID: 25360132 PMCID: PMC4199454 DOI: 10.3389/fmicb.2014.00541] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/29/2014] [Indexed: 01/04/2023] Open
Abstract
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.
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Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Department of Bioscience, Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Jörg Schnecker
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Birgit Wild
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Petr Čapek
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Vigdis L. Torsvik
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
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Aviles-Jimenez F, Vazquez-Jimenez F, Medrano-Guzman R, Mantilla A, Torres J. Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer. Sci Rep 2014; 4:4202. [PMID: 24569566 PMCID: PMC3935187 DOI: 10.1038/srep04202] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 02/10/2014] [Indexed: 02/07/2023] Open
Abstract
We aimed to characterize microbiota of the gastric mucosa as it progress to intestinal type of cancer. Study included five patients each of non-atrophic gastritis (NAG), intestinal metaplasia (IM) and intestinal-type gastric cancer (GC). Gastric tissue was obtained and DNA extracted for microbiota analyses using the microarray G3 PhyloChip. Bacterial diversity ranged from 8 to 57, and steadily decreased from NAG to IM to GC (p = 0.004). A significant microbiota difference was observed between NAG and GC based on Unifrac-presence/absence and weighted-Unifrac-abundance metrics of 283 taxa (p < 0.05). HC-AN analyses based on presence/absence of 238 taxa revealed that GC and NAG grouped apart, whereas IM overlapped with both. An ordinated analyses based on weighted-Unifrac distance given abundance of 44 taxa showing significance across categories revealed significant microbiota separation between NAG and GC. This study is the first to show a gradual shift in gastric microbiota profile from NAG to IM to GC.
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Affiliation(s)
| | - Flor Vazquez-Jimenez
- Unidad de Investigación en Enfermedades Infecciosas, Tubo Digestivo Alto, UMAE Oncologia
| | | | - Alejandra Mantilla
- Servicio de Patologia, UMAE Oncologia, Centro Medico Nacional SXXI, Mexico City
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, Tubo Digestivo Alto, UMAE Oncologia
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35
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Guo X, Wang C, Sun F, Zhu W, Wu W. A comparison of microbial characteristics between the thermophilic and mesophilic anaerobic digesters exposed to elevated food waste loadings. BIORESOURCE TECHNOLOGY 2013; 152:420-428. [PMID: 24316484 DOI: 10.1016/j.biortech.2013.11.012] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/30/2013] [Accepted: 11/07/2013] [Indexed: 06/02/2023]
Abstract
Thermophilic and mesophilic anaerobic digestion reactors (TR and MR) using food waste as substrate were compared with emphasis on microbial responses to increasing organic loading rate (OLR). At OLR ranging from 1.0 to 2.5 g VS L(-1) d(-1), MR exhibited more stable performance compared to TR in terms of methane yield. Amplicons pyrosequencing results revealed the distinct microbial dynamics in the two reactors. Primarily, MR had greater richness and evenness of bacteria species. With OLR elevated, larger shifts of bacterial phylogeny were observed in MR; Methanosaeta dominated in archaeal community in MR while Methanothermobacter and Methanoculleus were favored in TR. The high functional redundancy in bacterial community integrated with acetoclastic methanogenesis in MR resulted in its better performance; whereas delicate interactions between hydrogen-producer and hydrogenotrophic methanogens in TR were much more prone to disruption. These results are conductive to understanding the microbial mechanisms of low methane yield during food waste anaerobic digestion.
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Affiliation(s)
- Xiaohui Guo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Cheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Faqian Sun
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weijing Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weixiang Wu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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36
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Shah V, Zakrzewski M, Wibberg D, Eikmeyer F, Schlüter A, Madamwar D. Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. MICROBIAL ECOLOGY 2013; 66:533-550. [PMID: 23728164 DOI: 10.1007/s00248-013-0244-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878′; E 072°38.478′), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental cleanup projects.
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Affiliation(s)
- Varun Shah
- Museo Nacional de Ciencias Naturales-CSIC, C/Serrano 115 bis., 28006, Madrid, Spain,
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37
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Shah V, Zakrzewski M, Wibberg D, Eikmeyer F, Schlüter A, Madamwar D. Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges. MICROBIAL ECOLOGY 2013; 66:533-550. [PMID: 23797291 DOI: 10.1007/s00248-013-0253-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.
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Affiliation(s)
- Varun Shah
- BRD School of Biosciences, Sardar Patel University, Sardar Patel Maidan, Vadtal Road, Satellite Campus, Vallabh Vidyanagar 388 120, Post Box No. 39, Anand, Gujarat, India,
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