701
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Mengesha WK, Powell SM, Evans KJ, Barry KM. Diverse microbial communities in non-aerated compost teas suppress bacterial wilt. World J Microbiol Biotechnol 2017; 33:49. [PMID: 28181116 DOI: 10.1007/s11274-017-2212-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/16/2017] [Indexed: 02/01/2023]
Abstract
Non-aerated compost teas (NCTs) are water extracts of composted organic materials and are used to suppress soil borne and foliar disease in many pathosystems. Greenhouse trials were used to test the effectiveness of NCTs to suppress potato bacterial wilt caused by Ralstonia solanacearum on plants grown in soils inoculated with a virulent isolate of the pathogen (biovar II). NCTs prepared from matured compost sources: agricultural waste (AWCT), vermicompost (VCT) and solid municipal waste (SMWCT) were evaluated at three initial application times (7 days before inoculation, at time of inoculation and 7 days after inoculation) prior to weekly applications, in a randomized complete-block design. AWCT applied initially at the time of inoculation resulted in the greatest disease suppression, with the disease severity index 2.5-fold less than the non-treated plants and the "area under the disease progress curve" (AUDPC) 3.2-fold less. VCT and SMWCT were less suppressive than AWCT regardless of initial application time. Next generation sequencing of the v4 region of 16S rRNA gene and the internal transcribed spacer region (ITS1) revealed that diversity and composition of the bacterial and fungal communities across the NCTs varied significantly. Dominant bacterial phyla such as Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia, Chloroflexi, Planctomycetes, Acidobacteria, and a fungal phylum Ascomycota were detected in all NCTs. AWCT had optimum physico-chemical measurements with higher bacterial Shannon diversity indices (H) and fungal richness (S) than the other treatments. We conclude that bacterial wilt of potatoes grown in controlled conditions can be suppressed by a non-aerated compost tea with a high microbial diversity when applied at planting and weekly thereafter.
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702
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Liu T, Jia T, Chen J, Liu X, Zhao M, Liu P. Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE. Braz J Microbiol 2017; 48:246-250. [PMID: 28256389 PMCID: PMC5470430 DOI: 10.1016/j.bjm.2017.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/08/2015] [Indexed: 01/10/2023] Open
Abstract
Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM) to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) profiles indicated that a strain of Pediococcus acidilactici (band 9) is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.
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Affiliation(s)
- Tengfei Liu
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
| | - Tianzhu Jia
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
| | - Jiangning Chen
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
| | - Xiaoyu Liu
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
| | - Minjie Zhao
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
| | - Pengpeng Liu
- Liaoning University of Traditional Chinese Medicine, College of Pharmacy, Key Laboratory of Processing Theory Analysis of State Administration of Traditional Chinese Medicine, Dalian, China
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703
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Li S, Peng C, Wang C, Zheng J, Hu Y, Li D. Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability. Microb Ecol 2017; 73:1-15. [PMID: 27538871 DOI: 10.1007/s00248-016-0827-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/27/2016] [Indexed: 06/06/2023]
Abstract
Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.
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Affiliation(s)
- Shuangshuang Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jiaoli Zheng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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704
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Abstract
Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes. The same is true for plant and fungal ITS sequences. The application of highly specific-primers suppressing co-amplification of these sequence contaminations is a good solution for this issue. Here, we describe a detailed protocol for assessing bacterial and fungal endophyte diversity in plants using these primers in combination with next-generation sequencing.
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Affiliation(s)
- Bernd Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Franziska Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
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705
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Schneider D, Wemheuer F, Pfeiffer B, Wemheuer B. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies. Methods Mol Biol 2017; 1539:13-22. [PMID: 27900681 DOI: 10.1007/978-1-4939-6691-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.
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Affiliation(s)
- Dominik Schneider
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Franziska Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Birgit Pfeiffer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Bernd Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
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706
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Ma J, Wang Z, Zhang J, Waite TD, Wu Z. Cost-effective Chlorella biomass production from dilute wastewater using a novel photosynthetic microbial fuel cell (PMFC). Water Res 2017; 108:356-364. [PMID: 27836177 DOI: 10.1016/j.watres.2016.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/26/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
While microalgae have been suggested as a promising substitute to conventional fossil fuels, their cost effective cultivation and harvesting constitutes a major challenge. In the work described here, a novel photosynthetic microbial fuel cell (PMFC) in which a stainless steel mesh with biofilm formed on it serves as both the cathode and filtration material has been developed. Results of this study reveal that, in addition to inducing oxygen reduction reactions under illumination, the biocathode is effective in preventing the washout of algae during continuous operation, resulting in retained biomass concentrations reaching 3.5-6.5 g L-1. The maximum output current density reached ∼200 mA m-2 under irradiation, which is comparable with recent PMFC studies. Microbial diversity analyses targeting 16S and 18S rRNA genes indicated that the eukaryotic species belonging to the genus Chlorella was able to sustain its community dominance (>96%) over other competing species over the course of the studies. In the absence of catalysts such as Pt, a consortium of photosynthetic organisms including plant growth-promoting bacteria such as Azospirillum and Rhizobium were overrepresented in the biofilm, with these organisms most likely contributing to cathodic electron transfer. Energy flow analysis suggested that the PMFC system held the potential to achieve theoretical energy balance in simultaneous algae production and wastewater treatment.
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Affiliation(s)
- Jinxing Ma
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China.
| | - Junyao Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China.
| | - T David Waite
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Zhichao Wu
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China.
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707
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Andrade MVF, Sakamoto IK, Corbi JJ, Silva EL, Varesche MBA. Effects of hydraulic retention time, co-substrate and nitrogen source on laundry wastewater anionic surfactant degradation in fluidized bed reactors. Bioresour Technol 2017; 224:246-254. [PMID: 27847235 DOI: 10.1016/j.biortech.2016.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 05/12/2023]
Abstract
The aim of this study was to evaluate the influence of hydraulic retention time (HRT) on linear alkylbenzene sulfonate (LAS) removal in fluidized bed reactors (FBRs). FBR1 (HRT of 8h) and FBR2 (HRT of 12h) were fed laundry wastewater with 18.6±4.1 to 27.1±5.6mg/L of LAS in the following conditions: ethanol and nitrate addition (Phases I, II and III), nitrate (Phase IV), ethanol (Phase V) and laundry wastewater (Phase VI). LAS removal was 93±12% (FBR1) and 99±2% (FBR2). In FBR1, nitrate influenced significantly on LAS removal (99±3% - Phase IV) compared to the phase without nitrate (90±15% - Phase V). In FBR1 the absence of ethanol was more favourable for LAS removal (99±3% - Phase IV) compared to ethanol addition (87±16% - Phase II). In FBR2, 99±2% LAS removal was found up to 436days. By microbial characterization were identified bacteria as Acinetobacter, Dechloromonas, Pseudomonas and Zoogloea.
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Affiliation(s)
- Marcus Vinicius Freire Andrade
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense Avenue 400, 13566-590 São Carlos, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense Avenue 400, 13566-590 São Carlos, SP, Brazil
| | - Juliano José Corbi
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense Avenue 400, 13566-590 São Carlos, SP, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luiz, Km 235, SP 310, 13565-905 São Carlos, SP, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense Avenue 400, 13566-590 São Carlos, SP, Brazil.
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708
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Rogers MB, Firek B, Shi M, Yeh A, Brower-Sinning R, Aveson V, Kohl BL, Fabio A, Carcillo JA, Morowitz MJ. Disruption of the microbiota across multiple body sites in critically ill children. Microbiome 2016; 4:66. [PMID: 28034303 PMCID: PMC5200963 DOI: 10.1186/s40168-016-0211-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/24/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets. RESULTS Bacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1-9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of "dominant" pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient. CONCLUSIONS We conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.
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Affiliation(s)
- Matthew B. Rogers
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brian Firek
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Min Shi
- Division of Pediatric General and Thoracic Surgery, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Rachel Brower-Sinning
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Victoria Aveson
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brittany L. Kohl
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Anthony Fabio
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Joseph A. Carcillo
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Michael J. Morowitz
- Division of Pediatric Surgery, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, 7th Floor Faculty Pavilion, Pittsburgh, PA 15244 USA
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709
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Song C, Wang B, Tan J, Zhu L, Lou D, Cen X. Comparative analysis of the gut microbiota of black bears in China using high-throughput sequencing. Mol Genet Genomics 2016; 292:407-414. [PMID: 28028611 DOI: 10.1007/s00438-016-1282-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022]
Abstract
The Asiatic black bear (Ursus thibetanus) is a protected species from eastern Asia. In China, the Asiatic black bear occurs in 17 provinces from northeast to southwest regions. To date, information on microbial diversity in the gut of the Asiatic black bears from different populations remains limited. To determine the species composition and community structure of the gut microbiota in the Asiatic black bear, we characterized 36 fecal samples from Sichuan, Yunnan, and Heilongjiang provinces, China, by pyrosequencing the 16S V3-V4 hypervariable regions using the Illumina Miseq platform. Results showed that Firmicutes and Proteobacteria were the predominant phyla in the samples, which were largely comprised Escherichia-Shigella, Peptostreptococcaceae_incertae_sedis, Turicibacter, Streptococcus, and Clostridium. By analyzing the community structure from these 36 samples, we found that there were significant differences in the species diversity and richness between Sichuan, Yunnan, and Heilongjiang populations. In conclusion, our results reveal the species composition and structure of the gut microbiota in captive black bears in China, and suggest that biogeography could affect the black bear' gut microbiota.
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Affiliation(s)
- Can Song
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China.
| | - Jun Tan
- School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, China.
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China.
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China
| | - Deshuai Lou
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China
| | - Xiaoxi Cen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Bioengineering College, Chongqing University, No. 174, Shapingba Main Street, Chongqing, 400030, China
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710
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Sierra-Garcia IN, Dellagnezze BM, Santos VP, Chaves B MR, Capilla R, Santos Neto EV, Gray N, Oliveira VM. Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales. Extremophiles 2016; 21:211-229. [PMID: 27915388 DOI: 10.1007/s00792-016-0897-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Abstract
Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.
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Affiliation(s)
- Isabel Natalia Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil. .,School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Bruna M Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
| | - Viviane P Santos
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
| | - Michel R Chaves B
- Institute of Chemistry, University of Campinas, Campinas, CEP13083-970, Brazil
| | - Ramsés Capilla
- PETROBRAS/R&D Center, Rio de Janeiro, CEP 21949-900, Brazil
| | | | - Neil Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Valeria M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
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711
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Zheng D, Chang Q, Li Z, Gao M, She Z, Wang X, Guo L, Zhao Y, Jin C, Gao F. Performance and microbial community of a sequencing batch biofilm reactor treating synthetic mariculture wastewater under long-term exposure to norfloxacin. Bioresour Technol 2016; 222:139-147. [PMID: 27716565 DOI: 10.1016/j.biortech.2016.09.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 05/07/2023]
Abstract
The performance and microbial community of a sequencing batch biofilm reactor (SBBR) treating synthetic mariculture wastewater were evaluated under long-term exposure to norfloxacin (NFX) due to the overuse of antibiotics during the mariculture. The COD and NH4+-N removals had no distinct change at 0-6mgL-1 NFX and were inhibited at 6-35mgL-1 NFX. The specific oxygen uptake rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) of the biofilm kept a decreasing tendency with the increase of NFX concentration from 0 to 35mgL-1. The presence of NFX promoted the microorganisms to secrete more extracellular polymeric substances (EPS) and affected the chemical compositions of EPS. The microbial richness and diversity showed some obvious variations at different NFX concentrations. The present results demonstrated that NFX inhibited the SBBR performance and should decrease the NFX dosage in the mariculture.
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Affiliation(s)
- Dong Zheng
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao 266100, China
| | - Qingbo Chang
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Zhiwei Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xuejiao Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Feng Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
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712
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Kasemodel MC, Lima JZ, Sakamoto IK, Varesche MBA, Trofino JC, Rodrigues VGS. Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data. Environ Monit Assess 2016; 188:698. [PMID: 27896584 DOI: 10.1007/s10661-016-5708-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60 g kg-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20 cm) is highly contaminated (I geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.
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Affiliation(s)
- Mariana Consiglio Kasemodel
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Jacqueline Zanin Lima
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Maria Bernadete Amancio Varesche
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Julio Cesar Trofino
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
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713
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Han CS, Martin MA, Dichosa AEK, Daughton AR, Frietze S, Kaplan H, Gurven MD, Alcock J. Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication. PeerJ 2016; 4:e2660. [PMID: 27833819 PMCID: PMC5101600 DOI: 10.7717/peerj.2660] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 10/05/2016] [Indexed: 01/21/2023] Open
Abstract
Background Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota. We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. Results The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes (p < 0.01) and fewer Proteobacteria (p < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g. Neisseria, Gemella, Rothia, Actinomyces, Fusobacterium, and Leptotrichia, were more abundant in mothers than in infants. Conclusions Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.
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Affiliation(s)
- Cliff S Han
- Bioscience Division, Los Alamos National LaborataoryLos Alamos, NM, USA
| | | | | | - Ashlynn R Daughton
- Analytics, Intelligence and Technology (A) Division, Los Alamos National Laborataory, Los Alamos, NM, USA
| | - Seth Frietze
- Department of Medical Laboratory and Radiation Sciences, University of Vermont, Burlington, VT, USA
| | - Hillard Kaplan
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA
| | - Michael D Gurven
- Department of Anthropology, University of California, Santa BarbaraSanta Barbara, CA, USA
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM, USA
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714
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Valverde-Pérez B, Wágner DS, Lóránt B, Gülay A, Smets BF, Plósz BG. Short-sludge age EBPR process - Microbial and biochemical process characterisation during reactor start-up and operation. Water Res 2016; 104:320-329. [PMID: 27570133 DOI: 10.1016/j.watres.2016.08.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/30/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
The new paradigm for used water treatment suggests the use of short solid retention times (SRT) to minimize organic substrate mineralization and to maximize resource recovery. However, little is known about the microbes and the underlying biogeochemical mechanisms driving these short-SRT systems. In this paper, we report the start-up and operation of a short-SRT enhanced biological phosphorus removal (EBPR) system operated as a sequencing batch reactor (SBR) fed with preclarified municipal wastewater, which is supplemented with propionate. The microbial community was analysed via 16S rRNA amplicon sequencing. During start-up (SRT = 8 d), the EBPR was removing up to 99% of the influent phosphate and completely oxidized the incoming ammonia. Furthermore, the sludge showed excellent settling properties. However, once the SRT was shifted to 3.5 days nitrification was inhibited and bacteria of the Thiothrix taxon proliferated in the reactor, thereby leading to filamentous bulking (sludge volume index up to SVI = 1100 mL/g). Phosphorus removal deteriorated during this period, likely due to the out-competition of polyphosphate accumulating organisms (PAO) by sulphate reducing bacteria (SRB). Subsequently, SRB activity was suppressed by reducing the anaerobic SRT from 1.2 day to 0.68 day, with a consequent rapid SVI decrease to ∼200 ml/g. The short-SRT EBPR effectively removed phosphate and nitrification was mitigated at SRT = 3 days and oxygen levels ranging from 2 to 3 mg/L.
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Affiliation(s)
- Borja Valverde-Pérez
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark.
| | - Dorottya S Wágner
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark
| | - Bálint Lóránt
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark
| | - Arda Gülay
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark
| | - Benedek Gy Plósz
- Department of Environmental Engineering (DTU Environment), Technical University of Denmark, Miljøvej, Building 115, DK-2800, Kgs. Lyngby, Denmark.
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715
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Ribière C, Beugnot R, Parisot N, Gasc C, Defois C, Denonfoux J, Boucher D, Peyretaillade E, Peyret P. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning. Methods Mol Biol 2016; 1399:167-82. [PMID: 26791503 DOI: 10.1007/978-1-4939-3369-3_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
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Affiliation(s)
- Céline Ribière
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Réjane Beugnot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Nicolas Parisot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Cyrielle Gasc
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Clémence Defois
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Jérémie Denonfoux
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
- Genoscreen, Campus de l'Institut Pasteur de Lille, 59000, Lille, France.
| | - Delphine Boucher
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Eric Peyretaillade
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
| | - Pierre Peyret
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
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716
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Ibekwe AM, Ma J, Murinda SE. Bacterial community composition and structure in an Urban River impacted by different pollutant sources. Sci Total Environ 2016; 566-567:1176-1185. [PMID: 27267715 DOI: 10.1016/j.scitotenv.2016.05.168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 05/13/2023]
Abstract
Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment.
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Affiliation(s)
- A Mark Ibekwe
- USDA-ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA.
| | - Jincai Ma
- USDA-ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China
| | - Shelton E Murinda
- Animal and Veterinary Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
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717
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Martirosyan V, Unc A, Miller G, Doniger T, Wachtel C, Steinberger Y. Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space. Microb Ecol 2016; 72:659-668. [PMID: 27450478 DOI: 10.1007/s00248-016-0822-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1). We found that the composition of bacterial and fungal orders is plant-type-specific, indicating that each plant type provides a suitable and unique microenvironment. The different adaptive ecophysiological properties of the three plant species and the differential effect on their associated microbial composition point to the role of adaptation in the shaping of microbial diversity. Overall, our findings suggest a link between plant ecophysiological adaptation as a "temporary host" and the biotic-community parameters in extreme xeric environments.
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Affiliation(s)
- Varsik Martirosyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Life Sciences International Postgraduate Educational Center, Acharyan 31 Str., Yerevan, 0040, Armenia
| | - Adrian Unc
- Boreal Ecosystems Research Initiative, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9, Canada
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Chaim Wachtel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yosef Steinberger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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718
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Pereira RA, Salvador AF, Dias P, Pereira MFR, Alves MM, Pereira L. Perspectives on carbon materials as powerful catalysts in continuous anaerobic bioreactors. Water Res 2016; 101:441-447. [PMID: 27295618 DOI: 10.1016/j.watres.2016.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/16/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
The catalytic effect of commercial microporous activated carbon (AC) and macroporous carbon nanotubes (CNT) is investigated in reductive bioreactions in continuous high rate anaerobic reactors, using the azo dye Acid Orange 10 (AO10) as model compound as electron acceptor and a mixture of VFA as electron donor. Size and concentration of carbon materials (CM) and hydraulic retention time (HRT) are assessed. CM increased the biological reduction rate of AO10, resulting in significantly higher colour removal, as compared to the control reactors. The highest efficiency, 98%, was achieved with a CNT diameter (d) lower than 0.25 mm, at a CNT concentration of 0.12 g per g of volatile solids (VS), a HRT of 10 h and resulted in a chemical oxygen demand (COD) removal of 85%. Reducing the HRT to 5 h, colour and COD removal in CM-mediated bioreactors were above 90% and 80%, respectively. In the control reactor, thought similar COD removal was achieved, AO10 decolourisation was just approximately 20%, demonstrating the ability of CM to significantly accelerate the reduction reactions in continuous bioreactors. AO10 reduction to the correspondent aromatic amines was proved by high performance liquid chromatography (HPLC). Colour decrease in the reactor treating a real effluent with CNT was the double comparatively to the reactor operated without CNT. The presence of AC in the reactor did not affect the microbial diversity, as compared to the control reactor, evidencing that the efficient reduction of AO10 was mainly due to AC rather than attributed to changes in the composition of the microbial communities.
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Affiliation(s)
- R A Pereira
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - A F Salvador
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - P Dias
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M F R Pereira
- Laboratório de Catálise e Materiais (LCM), Laboratório Associado LSRE/LCM, Departamento de Engenharia Química, Faculdade Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - M M Alves
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - L Pereira
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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719
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Rekadwad BN, Khobragade CN. Is the increase in oil pollution a possibility of the presence of diverse microorganisms? An experimental dataset on oil prevalent areas of Goa, India. Data Brief 2016; 9:8-12. [PMID: 27622205 DOI: 10.1016/j.dib.2016.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 11/22/2022] Open
Abstract
Survey data and wet lab reports presented in this paper were collected from Western coastlines of India from Goan beaches. Oil polluted areas were captured on camera as evidence for oil and tar pollution. Several microorganisms showing diverse characteristics such as pigment producers, salt tolerant and hydrocarbon resistance were isolated and cultured in the laboratory. The dataset presented in this paper supports “A case study on effects of oil spills and tar-ball pollution on beaches of Goa (India)” (Rekadwad and Khobragade, 2015) [1] and “Microbial diversity of oil spills and tar resistant bacteria isolated from beaches of Goa (India)” (Rekadwad and Khobragade, 2016) [2].
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720
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Savage AM, Hills J, Driscoll K, Fergus DJ, Grunden AM, Dunn RR. Microbial diversity of extreme habitats in human homes. PeerJ 2016; 4:e2376. [PMID: 27672493 PMCID: PMC5028791 DOI: 10.7717/peerj.2376] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/29/2016] [Indexed: 12/15/2022] Open
Abstract
High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.
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Affiliation(s)
- Amy M Savage
- Rutgers, The State University of New Jersey , Camden , United States
| | - Justin Hills
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases , Bethesda , MD , United States
| | - Katherine Driscoll
- Animal Management Department, The Wilds , Cumberland , OH , United States
| | - Daniel J Fergus
- Genomics and Microbiology, North Carolina Museum of Natural Sciences , Raleigh , NC , United States
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University , Raleigh , NC , United States
| | - Robert R Dunn
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University , Raleigh , NC , United States
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721
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Dao HT, Kuroda K, Nakahara N, Danshita T, Hatamoto M, Yamaguchi T. 16S rRNA gene-based comprehensive analysis of microbial community compositions in a full-scale leachate treatment system. J Biosci Bioeng 2016; 122:708-15. [PMID: 27594512 DOI: 10.1016/j.jbiosc.2016.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/16/2016] [Accepted: 06/07/2016] [Indexed: 11/20/2022]
Abstract
In this study, we performed a comprehensive analysis of microbial community compositions in leachate and leachate treatment system (14 processes) during dry and rainy seasons (from February to September and from October to January, respectively), at Khanh Son landfill site, Danang City, Vietnam. In this study, raw leachate in dry and rainy seasons was predominated by Arcobacter, Clostridia, Thermotogales, Methanobacteriaceae, and Methanosaeta. During the two seasons, the system had different microbial community compositions. Orders Methanobacteriales, Clostridiales, MBA08 (order-level clone cluster), and Thermotogales predominated the influent, anaerobic pond, and anoxic pond during the dry season, while Campylobacterales and Pseudomonadales orders were predominant in the anaerobic/anoxic systems during the rainy season. In the facultative pond, aerated ponds, sediment tanks, and polishing ponds, predominant orders during the dry season included Actinomycetales, "Saprospirales", Flavobacteriales, Rhizobiales, Rhodospirillales, Burkholderiales, and Alteromonadales; during the rainy season: Sphingobacteriales, Rickettsiales, Sphingomonadales, and Pseudomonadales. In the final post treatment (polishing ponds with vegetation), significant removal of organic matter, total nitrogen, and colour occurred, while nitrogen-fixing and root-associated or related organisms predominated. This suggested that the vegetation in the ponds was essential to achieve the sufficient leachate treatment.
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722
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Paulino-Lima IG, Fujishima K, Navarrete JU, Galante D, Rodrigues F, Azua-Bustos A, Rothschild LJ. Extremely high UV-C radiation resistant microorganisms from desert environments with different manganese concentrations. J Photochem Photobiol B 2016; 163:327-36. [PMID: 27614243 DOI: 10.1016/j.jphotobiol.2016.08.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 08/10/2016] [Indexed: 12/25/2022]
Abstract
Desiccation resistance and a high intracellular Mn/Fe ratio contribute to ionizing radiation resistance of Deinococcus radiodurans. We hypothesized that this was a general phenomenon and thus developed a strategy to search for highly radiation-resistant organisms based on their natural environment. While desiccation is a typical feature of deserts, the correlation between radiation resistance and the intracellular Mn/Fe ratio of indigenous microorganisms or the Mn/Fe ratio of the environment, has not yet been described. UV-C radiation is highly damaging to biomolecules including DNA. It was used in this study as a selective tool because of its relevance to early life on earth, high altitude aerobiology and the search for life beyond Earth. Surface soil samples were collected from the Sonoran Desert, Arizona (USA), from the Atacama Desert in Chile and from a manganese mine in northern Argentina. Microbial isolates were selected after exposure to UV-C irradiation and growth. The isolates comprised 28 genera grouped within six phyla, which we ranked according to their resistance to UV-C irradiation. Survival curves were performed for the most resistant isolates and correlated with their intracellular Mn/Fe ratio, which was determined by ICP-MS. Five percent of the isolates were highly resistant, including one more resistant than D. radiodurans, a bacterium generally considered the most radiation-resistant organism, thus used as a model for radiation resistance studies. No correlation was observed between the occurrence of resistant microorganisms and the Mn/Fe ratio in the soil samples. However, all resistant isolates showed an intracellular Mn/Fe ratio much higher than the sensitive isolates. Our findings could represent a new front in efforts to harness mechanisms of UV-C radiation resistance from extreme environments.
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Affiliation(s)
| | - Kosuke Fujishima
- University Affiliated Research Center, NASA Ames Research Center, Moffett Field, CA, 94035-0001, USA
| | - Jesica Urbina Navarrete
- University Affiliated Research Center, NASA Ames Research Center, Moffett Field, CA, 94035-0001, USA
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory, Campinas, 13083-970, Brazil
| | - Fabio Rodrigues
- Institute of Chemistry, University of São Paulo, 05508-000, Brazil
| | - Armando Azua-Bustos
- Centro de Investigación Biomédica, UniversidadAutónoma de Chile, Santiago, 8910060, Chile
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Leung MHY, Chan KCK, Lee PKH. Skin fungal community and its correlation with bacterial community of urban Chinese individuals. Microbiome 2016; 4:46. [PMID: 27558504 PMCID: PMC4997687 DOI: 10.1186/s40168-016-0192-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND High-throughput sequencing has led to increased insights into the human skin microbiome. Currently, the majority of skin microbiome investigations are limited to characterizing prokaryotic communities, and our understanding of the skin fungal community (mycobiome) is limited, more so for cohorts outside of the western hemisphere. Here, the skin mycobiome across healthy Chinese individuals in Hong Kong are characterized. RESULTS Based on a curated fungal reference database designed for skin mycobiome analyses, previously documented common skin colonizers are also abundant and prevalent in this cohort. However, genera associated with local terrains, food, and medicine are also detected. Fungal community composition shows interpersonal (Bray-Curtis ANOSIM = 0.398) and household (Bray-Curtis ANOSIM = 0.134) clustering. Roles of gender and age on diversity analyses are test- and site-specific, and, contrary to bacteria, the effect of household on fungal community composition dissimilarity between samples is insignificant. Site-specific, cross-domain positive and negative correlations at both community and operational taxonomic unit levels may uncover potential relationships between fungi and bacteria on skin. CONCLUSIONS The studied Chinese population presents similar major fungal skin colonizers that are also common in western populations, but local outdoor environments and lifestyles may also contribute to mycobiomes of specific cohorts. Cohabitation plays an insignificant role in shaping mycobiome differences between individuals in this cohort. Increased understanding of fungal communities of non-western cohorts will contribute to understanding the size of the global skin pan-mycobiome, which will ultimately help understand relationships between environmental exposures, microbial populations, and the health of global humans.
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Affiliation(s)
- Marcus H. Y. Leung
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | | | - Patrick K. H. Lee
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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724
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Scanlan PD, Knight R, Song SJ, Ackermann G, Cotter PD. Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infect Genet Evol 2016; 45:95-97. [PMID: 27545648 DOI: 10.1016/j.meegid.2016.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/04/2016] [Accepted: 08/17/2016] [Indexed: 02/08/2023]
Abstract
The human gut is host to a diversity of microorganisms including the single-celled microbial eukaryote Blastocystis. Although Blastocystis has a global distribution, there is dearth of information relating to its prevalence and diversity in many human populations. The mode of Blastocystis transmission to humans is also insufficiently characterised, however, it is speculated to vary between different populations. Here we investigated the incidence and genetic diversity of Blastocystis in a US population and also the possibility of Blastocystis human-human transmission between healthy individuals using family units (N=50) living in Boulder, Colorado as our sample-set. Ten of the 139 (~7%) individuals in our dataset were positive for Blastocystis, nine of whom were adults and one individual belonging to the children/adolescents group. All positive cases were present in different family units. A number of different Blastocystis subtypes (species) were detected with no evidence of mixed infections. The prevalence of Blastocystis in this subset of the US population is comparatively low relative to other industrialised populations investigated to date; however, subtype diversity was largely consistent with that previously reported in studies of European populations. The distribution of Blastocystis within family units indicates that human-human transmission is unlikely to have occurred within families that participated in this study. It is not unexpected that given the world-wide variation in human living conditions and lifestyles between different populations, both the prevalence of Blastocystis and its mode of transmission to humans may vary considerably.
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Affiliation(s)
- Pauline D Scanlan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland.
| | - Rob Knight
- Department of Pediatrics and Computer Science & Engineering, University of California at San Diego, San Diego, CA, USA
| | - Se Jin Song
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics and Computer Science & Engineering, University of California at San Diego, San Diego, CA, USA
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland
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725
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Babatunde AO, Miranda-CasoLuengo R, Imtiaz M, Zhao YQ, Meijer WG. Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems. J Environ Sci (China) 2016; 46:38-46. [PMID: 27521934 DOI: 10.1016/j.jes.2015.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/30/2015] [Accepted: 02/16/2015] [Indexed: 06/06/2023]
Abstract
This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance.
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Affiliation(s)
- A O Babatunde
- Hydro-environmental Research Centre, Institute of Environment and Sustainability, Cardiff School of Engineering, Cardiff University, Queen's Buildings, The Parade, Cardiff, CF24 3AA, UK; UCD School of Civil, Structural and Environmental Engineering, Newstead Building, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Raul Miranda-CasoLuengo
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mehreen Imtiaz
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Y Q Zhao
- UCD School of Civil, Structural and Environmental Engineering, Newstead Building, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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726
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Sözen S, Teksoy Başaran S, Akarsubaşı A, Ergal I, Insel G, Karaca C, Orhon D. Toward a novel membrane process for organic carbon removal-fate of slowly biodegradable substrate in super fast membrane bioreactor. Environ Sci Pollut Res Int 2016; 23:16230-16240. [PMID: 27154840 DOI: 10.1007/s11356-016-6795-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
The study tested the performance of super fast membrane bioreactor (SFMBR) using starch as a slowly biodegradable substrate, exploring the fate of starch, and the response of the microbial community. SFMBR was operated at extremely low sludge ages of 0.5-2.0 days, with a hydraulic retention time of 1.0 h. Average values for permeate chemical oxygen demand (COD) always remained in the narrow range between 14 and 18 mg/L, regardless of the selected mode of MBR operation at different sludge ages. Soluble COD levels in the reactor were consistently higher than the corresponding permeate COD. Parameters defining process kinetics, determined by model calibration of oxygen uptake rate (OUR) profiles, varied as a function of sludge age. Model simulation of SFMBR performance indicated total removal of hydrolysis products so that permeate COD consisted of residual microbial products. PCR-DGGE experiments revealed significant shifts in the composition of the microbial community imposed by variations in the sludge age, reflecting on corresponding process kinetics.
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Affiliation(s)
- S Sözen
- Faculty of Civil Engineering, Environmental Engineering Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey.
| | - S Teksoy Başaran
- Faculty of Civil Engineering, Environmental Engineering Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
| | - A Akarsubaşı
- Faculty of Science and Letters, Molecular Biology and Genetics Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
| | - I Ergal
- Faculty of Science and Letters, Molecular Biology and Genetics Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
| | - G Insel
- Faculty of Civil Engineering, Environmental Engineering Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
| | - C Karaca
- Faculty of Civil Engineering, Environmental Engineering Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
| | - D Orhon
- Faculty of Civil Engineering, Environmental Engineering Department, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey
- The Science Academy, 34353, Beşiktaş, Istanbul, Turkey
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727
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Abstract
BACKGROUND Diabetes, obesity, and the metabolic syndrome are multifactorial diseases dependent on a complex interaction of host genetics, diet, and other environmental factors. Increasing evidence places gut microbiota as important modulators of the crosstalk between diet and development of obesity and metabolic dysfunction. In addition, host genetics can have important impact on the composition and function of gut microbiota. Indeed, depending on the genetic background of the host, diet and other environmental factors may produce different changes in gut microbiota, have different impacts on host metabolism, and create different interactions between the microbiome and the host. SCOPE OF REVIEW In this review, we highlight how appropriate animal models can help dissect the complex interaction of host genetics with the gut microbiome and how diet can lead to different degrees of weight gain, levels of insulin resistance, and metabolic outcomes, such as diabetes, in different individuals. We also discuss the challenges of identifying specific disease-associated microbiota and the limitations of simple metrics, such as phylogenetic diversity or the ratio of Firmicutes to Bacteroidetes. MAJOR CONCLUSIONS Understanding these complex interactions will help in the development of novel treatments for microbiome-related metabolic diseases. This article is part of a special issue on microbiota.
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728
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Kambura AK, Mwirichia RK, Kasili RW, Karanja EN, Makonde HM, Boga HI. Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol 2016; 16:136. [PMID: 27388368 DOI: 10.1186/s12866-016-0748-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/15/2016] [Indexed: 02/02/2023] Open
Abstract
Background Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi. Methods Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1 °C and from Little Magadi “Nasikie eng’ida” (temperature of 81 °C and 83.6 °C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 – V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package. Results Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 % 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33–50 %), Firmicutes 3.52–28.92 %, Bacteroidetes (3.45–26.44 %), Actinobacteria (0.98–28.57 %) and Euryarchaeota (3.55–34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81–83 °C). Conclusion There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users.
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729
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Kong Z, Li L, Feng C, Dong S, Chen N. Comparative investigation on integrated vertical-flow biofilters applying sulfur-based and pyrite-based autotrophic denitrification for domestic wastewater treatment. Bioresour Technol 2016; 211:125-135. [PMID: 27015019 DOI: 10.1016/j.biortech.2016.03.083] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/13/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Two parallel biofilters applying sulfur/pyrite-based autotrophic denitrification were investigated for removing COD, TP and TN by a coordinated process. Results demonstrated good performance by removing 86.32% vs 87.14% COD and 92.56% vs 89.65% NH4(+)-N. Biofilter with sulfur (BS) was superior on nitrate (89.74% vs 80.72%) and TN removal (83.18% vs 70.42%) while biofilter with pyrite (BP) was better on TP removal (82.58% vs 77.40%) and maintaining sulfate (27.56mgL(-1) vs 41.55mgL(-1)) and pH (7.13 vs 6.31). Water-permeable adsorbents lowered clogging risk and buffered loading. Clone library revealed reasons of diversities, pH variation and sulfate accumulation of both biofilters. Sulfur was efficient on denitrification but whose byproducts were troublesome, pyrite produced less byproduct but which was sensitive to organics. This research was the first attempt to systematically compare two promising alternatives and their merits/demerits for rural wastewater on-site treatment.
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Affiliation(s)
- Zhe Kong
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Lu Li
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Shanshan Dong
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Nan Chen
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
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730
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Lin Q, He G, Rui J, Fang X, Tao Y, Li J, Li X. Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion. Microb Cell Fact 2016; 15:96. [PMID: 27260194 PMCID: PMC4893225 DOI: 10.1186/s12934-016-0491-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/23/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). RESULTS Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. CONCLUSIONS The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guihua He
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junpeng Rui
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yong Tao
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Nuansawan N, Boonnorat J, Chiemchaisri W, Chiemchaisri C. Effect of hydraulic retention time and sludge recirculation on greenhouse gas emission and related microbial communities in two-stage membrane bioreactor treating solid waste leachate. Bioresour Technol 2016; 210:35-42. [PMID: 26860618 DOI: 10.1016/j.biortech.2016.01.109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
Methane (CH4) and nitrous oxide (N2O) emissions and responsible microorganisms during the treatment of municipal solid waste leachate in two-stage membrane bioreactor (MBR) was investigated. The MBR system, consisting of anaerobic and aerobic stages, were operated at hydraulic retention time (HRT) of 5 and 2.5days in each reactor under the presence and absence of sludge recirculation. Organic and nitrogen removals were more than 80% under all operating conditions during which CH4 emission were found highest under no sludge recirculation condition at HRT of 5days. An increase in hydraulic loading resulted in a reduction in CH4 emission from anaerobic reactor but an increase from the aerobic reactor. N2O emission rates were found relatively constant from anaerobic and aerobic reactors under different operating conditions. Diversity of CH4 and N2O producing microorganisms were found decreasing when hydraulic loading rate to the reactors was increased.
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Affiliation(s)
- Nararatchporn Nuansawan
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Jarungwit Boonnorat
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Wilai Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Chart Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand.
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732
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Zhao J, Chen X, Bao L, Bao Z, He Y, Zhang Y, Li J. Correlation between microbial diversity and toxicity of sludge treating synthetic wastewater containing 4-chlorophenol in sequencing batch reactors. Chemosphere 2016; 153:138-145. [PMID: 27016808 DOI: 10.1016/j.chemosphere.2016.01.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 01/12/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
The relationship between microbial diversity and sludge toxicity in the biotreatment of refractory wastewater was investigated. Synthetic wastewater containing 4-chlorophenol (4-CP) was treated by an activated sludge using a sequencing batch bioreactor (SBR). At the end of a single SBR cycle, a stable operation stage was reached when the 4-CP was not detected both in aqueous and sludge phases and the effluent COD was maintained at approximately 70 mg L(-1) for the blank and control sludge groups. Then, the diversity of the microorganisms and the sludge toxicity were measured. The results showed that the Microtox acute toxicity of the control sludge was higher than those of the blank sludge. The difference analysis of the microbial diversity between the blank and control sludge indicated that the sludge toxicity was closely related to microbial diversity.
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Affiliation(s)
- Jianguo Zhao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China; Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Eduaction, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang, 453007, China
| | - Xiurong Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China.
| | - Linlin Bao
- Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Eduaction, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang, 453007, China
| | - Zheng Bao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Yixuan He
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuying Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiahui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, 200237, China
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733
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Sinimol S, Sarika AR, Jayakumaran Nair A. Diversity and antagonistic potential of marine microbes collected from south-west coast of India. 3 Biotech 2016; 6:7. [PMID: 28330077 PMCID: PMC4697912 DOI: 10.1007/s13205-015-0318-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/14/2015] [Indexed: 12/01/2022] Open
Abstract
The diversity of some of the culturable microorganisms associated with marine flora and fauna collected off Vizhinjam and Mulloor coast of South India was evaluated and their bioactive production potential determined. From a total of 24 bacteria, 4 actinomycetes and 8 fungi isolated from diverse marine sources, five bacterial species-BLM3, BSP2, BCS1, BCS4 and BMA6 showed inhibitory activity against at least one of the tested pathogens viz., Klebsiella pneumonia KU1, Pseudomonas aeruginosa VL3, Salmonella enterica typhimurium MTCC 98, Escherichia coli MTCC 40, Micrococcus luteus MTCC 105, Staphylococcus simulans MTCC 3610, Proteus vulgaris MTCC 426, Vibrio fluvialis, Vibrio sp. P3a and Vibrio sp. P3b. The isolated actinomycetes and fungi did not produce significant inhibition zones against the tested pathogens; however, the macroalgal isolated actinomycetes strain AMA1 produced reddish pigment in Starch Casein medium which remained stable till the stationary phase of growth. The marine sediment isolate BCS4, identified as Bacillus sp. showed wide spectrum of activity against the tested Gram positive bacteria, S. simulans MTCC 3610 and Gram negative bacteria, Proteus vulgaris with zone of inhibitions of 25 and 11 mm respectively. Better extraction of the bioactive compound was obtained with ethyl acetate when compared with methanol, benzene and hexane and TLC analysis revealed the presence of an active compound. The 16SrRNA sequencing confirmed the potent strain belong to Bacillus sp. and hence designated Bacillus sp. BCS4.
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734
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Zhang L, Jia Y, Zhang X, Feng X, Wu J, Wang L, Chen G. Wheat straw: An inefficient substrate for rapid natural lignocellulosic composting. Bioresour Technol 2016; 209:402-406. [PMID: 26980627 DOI: 10.1016/j.biortech.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
Composting is a promising method for the management of agricultural wastes. However, results for wheat straw composts with different carbon-to-nitrogen ratios revealed that wheat straw was only partly degraded after composting for 25days, with hemicellulose and cellulose content decreasing by 14% and 33%, respectively. No significant changes in community structure were found after composting according to 454-pyrosequencing. Bacterial communities were represented by Proteobacteria and Bacteroidetes throughout the composting process, including relatively high abundances of pathogenic microbes such as Pseudomonas and Flexibacter, suggesting that innocent treatment of the composts had not been achieved. Besides, the significant lignocellulose degrader Thermomyces was not the exclusively dominant fungus with relative abundance only accounting for 19% of fungal communities. These results indicated that comparing with maize straw, wheat straw was an inefficient substrate for rapid natural lignocellulose-based composting, which might be due to the recalcitrance of wheat straw.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yangyang Jia
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xiaomei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | | | | | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.
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735
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Bissett A, Fitzgerald A, Court L, Meintjes T, Mele PM, Reith F, Dennis PG, Breed MF, Brown B, Brown MV, Brugger J, Byrne M, Caddy-Retalic S, Carmody B, Coates DJ, Correa C, Ferrari BC, Gupta VVSR, Hamonts K, Haslem A, Hugenholtz P, Karan M, Koval J, Lowe AJ, Macdonald S, McGrath L, Martin D, Morgan M, North KI, Paungfoo-Lonhienne C, Pendall E, Phillips L, Pirzl R, Powell JR, Ragan MA, Schmidt S, Seymour N, Snape I, Stephen JR, Stevens M, Tinning M, Williams K, Yeoh YK, Zammit CM, Young A. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience 2016; 5:21. [PMID: 27195106 PMCID: PMC4870752 DOI: 10.1186/s13742-016-0126-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 05/02/2016] [Indexed: 01/27/2023] Open
Abstract
Background Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. Findings BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’. Conclusions Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.
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Affiliation(s)
- Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania Australia
| | | | | | - Thys Meintjes
- Centre for Comparative Genomics, Murdoch University, Perth, Western Australia Australia
| | - Pauline M Mele
- Victorian Department of Economic Development, Jobs, Transport and Resources and La Trobe University, Agribio Centre, Bundoora, Victoria 3083 Australia
| | - Frank Reith
- CSIRO Land and Water, Adelaide, South Australia Australia ; School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | - Paul G Dennis
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | - Belinda Brown
- Parks Australia, Department of the Environment, Canberra, ACT 2601 Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales 2052 Australia
| | - Joel Brugger
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia
| | - Stefan Caddy-Retalic
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | | | - David J Coates
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia
| | - Carolina Correa
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 Australia
| | | | - Kelly Hamonts
- CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia ; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Asha Haslem
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072 Australia ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Mirko Karan
- Australian SuperSite Network, James Cook University, Townsville, Queensland Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | - Andrew J Lowe
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | | | - Leanne McGrath
- Australian Genome Research Facility Ltd, Adelaide, South Australia Australia
| | - David Martin
- Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia
| | - Matt Morgan
- CSIRO Land and Water, Canberra, ACT Australia
| | - Kristin I North
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | | | - Elise Pendall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Lori Phillips
- DEDJTR Rutherglen, Melbourne, Victoria Australia ; Agriculture and Agri-food Canada, Science and Technology branch, 2585 County Road 20, Harrow, ON N0R 1G0 Canada
| | - Rebecca Pirzl
- Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Nicole Seymour
- Department of Agriculture and Fisheries, Brisbane, Queensland Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and Communities, 203 Channel Highway, Kingston, Tasmania 7050 Australia
| | - John R Stephen
- Australian Genome Research Facility Ltd, Adelaide, South Australia Australia
| | - Matthew Stevens
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | - Matt Tinning
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | | | - Yun Kit Yeoh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072 Australia ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Carla M Zammit
- University of Queensland, Earth Sciences, St Lucia, Brisbane, Queensland 4072 Australia
| | - Andrew Young
- CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia
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736
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Shen D, Wang K, Yin J, Chen T, Yu X. Effect of phosphoric acid as a catalyst on the hydrothermal pretreatment and acidogenic fermentation of food waste. Waste Manag 2016; 51:65-71. [PMID: 26965213 DOI: 10.1016/j.wasman.2016.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/11/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
The hydrothermal method was applied to food waste (FW) pretreatment with phosphoric acid as a catalyst. The content of soluble substances such as protein and carbohydrate in the FW increased after the hydrothermal pretreatment with phosphoric acid addition (⩽5%). The SCOD approached approximately 29.0g/L in 5% phosphoric acid group, which is almost 65% more than the original FW. The hydrothermal condition was 160°C for 10min, which means that at least 40% of energy and 60% of reaction time were saved to achieve the expected pretreatment effect. Subsequent fermentation tests showed that the optimal dosage of phosphoric acid was 3% with a VFA yield of 0.763g/gVSremoval, but the increase in salinity caused by phosphoric acid could adversely affect the acidogenesis. With an increase in the quantity of phosphoric acid, among the VFAs, the percentage of propionic acid decreased and that of butyric acid increased. The PCR-DGGE analysis indicated that the microbial diversity could decrease with excessive phosphoric acid, which resulted in a low VFA yield.
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Affiliation(s)
- Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, PR China
| | - Kun Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, PR China; CCTEG Hangzhou Environmental Research Institute, Hangzhou 311200, PR China
| | - Jun Yin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, PR China.
| | - Ting Chen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, PR China
| | - Xiaoqin Yu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, PR China
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737
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Steinert G, Taylor MW, Deines P, Simister RL, de Voogd NJ, Hoggard M, Schupp PJ. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity. PeerJ 2016; 4:e1936. [PMID: 27114882 PMCID: PMC4841226 DOI: 10.7717/peerj.1936] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/23/2016] [Indexed: 01/03/2023] Open
Abstract
Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.
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Affiliation(s)
- Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter Deines
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Rachel L Simister
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | - Michael Hoggard
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg , Wilhelmshaven , Germany
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738
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Finley SJ, Pechal JL, Benbow ME, Robertson BK, Javan GT. Microbial Signatures of Cadaver Gravesoil During Decomposition. Microb Ecol 2016; 71:524-529. [PMID: 26748499 DOI: 10.1007/s00248-015-0725-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.
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Affiliation(s)
- Sheree J Finley
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - B K Robertson
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Gulnaz T Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, 915 S. Jackson St., Hatch Hall Building Room 251, Montgomery, AL, 36104, USA.
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739
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Li CY, Zhang D, Li XX, Mbadinga SM, Yang SZ, Liu JF, Gu JD, Mu BZ. The biofilm property and its correlationship with high-molecular-weight polyacrylamide degradation in a water injection pipeline of Daqing oilfield. J Hazard Mater 2016; 304:388-399. [PMID: 26595898 DOI: 10.1016/j.jhazmat.2015.10.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/25/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
Biofilms increase dragging force for liquid transportation, cause power consumption, and result in equipment corrosion in polymer-flooding oilfields. To reveal the responsible microorganisms for biofilm formation and stability of high-molecular-weight polyacrylamide (PAM), a biofilm, developed on the sieve of a piston plunger pump in a water transport and injection pipeline with partial hydrolyzed polyacrylamide (HPAM) in Daqing Oilfield, was collected and analyzed by molecular microbiology, chemical and physical methods. Diverse bacterial groups (11 families) were detected in the biofilm, including Pseudomonadaceae, Rhodocyclaceae, Desulfobulbaceae, Alcaligenaceae, Comamonadaceae, Oxalobacteraceae, Bacteriovoracaceae, Campylobacteraceae, Flavobacteriaceae, Clostridiales Incertae Sedis XIII and Moraxellaceae. Three archaeal orders of methanogens including Methanomicrobiales, Methanosarcinales and Thermoplasmatales were also detected separately. HPAM was degraded into lower molecular weight polymers and organic fragments with its amide groups hydrolyzed into carboxylic groups by the microorganisms. The microenvironment of the biofilm contained diverse bacterial and archaeal communities, correlating with the extracellular polymeric substance (EPS) and HPAM biodegradation. The results are helpful to provide information for biofilm control in oil fields.
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Affiliation(s)
- Cai-Yun Li
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Dong Zhang
- The fourth oil production Company of Daqing Oilfield Limited Company, PetroChina, Daqing 163511, Heilongjiang, PR China.
| | - Xiao-Xiao Li
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Serge Maurice Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China.
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China; Shanghai Collaborative Innovation Center of Biomanufacturing Technology, Shanghai 200237, PR China.
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740
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Kim NK, Oh S, Liu WT. Enrichment and characterization of microbial consortia degrading soluble microbial products discharged from anaerobic methanogenic bioreactors. Water Res 2016; 90:395-404. [PMID: 26771162 DOI: 10.1016/j.watres.2015.12.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 12/05/2015] [Accepted: 12/12/2015] [Indexed: 05/25/2023]
Abstract
Soluble microbial products (SMP) produced in bioprocesses have been known as a main cause to decrease treatment efficiency, lower effluent quality, and promote membrane fouling in water reclamation plants. In this study, biological degradation of SMP using selectively enriched microbial consortia in a down-flow hanging sponge (DHS) reactor was introduced to remove SMP discharged from anaerobic methanogenic reactors. On average, 68.9-87.5% SMP removal was achieved by the enriched microbial consortia in the DHS reactor for >800 days. The influent SMP fed to the DHS reactor exhibited a bimodal molecular weight (MW) distribution with 14-20 kDa and <4 kDa. Between these two types of SMP, the small MW SMP were biodegraded in the upper part of the reactor, together with most of the large MW SMP. Using 16S rRNA gene pyrosequencing technology, the microbial community composition and structure were characterized and correlated with operational factors, such as hydraulic retention time, organic loading rate, and removal of soluble chemical oxygen demand at different depths of the reactor, by performing network and redundancy analyses. The results revealed that Saprospiraceae was strongly correlated to the increasing SMP loading condition, indicating positive co-occurrences with neighboring bacterial populations. Different microbial diversity along with the depth of the reactor implies that stratified microbial communities could participate in the process of SMP degradation. Taken together, these observations indicate that the spatial and temporal variability of the enriched microbial community in the DHS reactor could effectively treat SMP with respect to changes in the operational factors.
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Affiliation(s)
- Na-Kyung Kim
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave., Urbana, IL 61801-2352, USA
| | - Seungdae Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave., Urbana, IL 61801-2352, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave., Urbana, IL 61801-2352, USA.
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741
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Pendyala B, Chaganti SR, Lalman JA, Heath DD. Optimizing the performance of microbial fuel cells fed a combination of different synthetic organic fractions in municipal solid waste. Waste Manag 2016; 49:73-82. [PMID: 26777306 DOI: 10.1016/j.wasman.2015.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/25/2015] [Accepted: 12/31/2015] [Indexed: 06/05/2023]
Abstract
The objective of this study was to establish the impact of different steam exploded organic fractions in municipal solid waste (MSW) on electricity production using microbial fuel cells (MFCs). In particular, the influence of individual steam exploded liquefied waste components (food waste (FW), paper-cardboard waste (PCW) and garden waste (GW)) and their blends on chemical oxygen demand (COD) removal, columbic efficiency (CE) and microbial diversity was examined using a mixture design. Maximum power densities from 0.56 to 0.83 W m(-2) were observed for MFCs fed with different feedstocks. The maximum COD removed and minimum CE were observed for a GW feed. However, a reverse trend (minimum COD removed and maximum CE) was observed for the FW feed. A maximum COD removal (78%) accompanied with a maximum CE (24%) was observed for a combined feed of FW, PCW plus GW in a 1:1:1 ratio. Lactate, the major byproduct detected, was unutilized by the anodic biofilm community. The organic fraction of municipal solid waste (OFMSW) could serve as a potential feedstock for electricity generation in MFCs; however, elevated protein levels will lead to reduced COD removal. The microbial communities in cultures fed FW and PCW was highly diversified; however, the communities in cultures fed FW or a feed mixture containing high FW levels were similar and dominated by Bacteroidetes and β-proteobacteria.
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Affiliation(s)
- Brahmaiah Pendyala
- Department of Civil and Environmental Engineering, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada
| | - Jerald A Lalman
- Department of Civil and Environmental Engineering, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada.
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; Department of Biological Sciences, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada
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742
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Liu J, Liu W, Wang F, Kerr P, Wu Y. Redox zones stratification and the microbial community characteristics in a periphyton bioreactor. Bioresour Technol 2016; 204:114-121. [PMID: 26773955 DOI: 10.1016/j.biortech.2016.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Bioremediation techniques based on microorganisms have been widely applied to treat polluted surface water, but the efficiencies have been limited, especially in deep and static waters. Microbial aggregates, known as periphyton, were introduced into a tank bioreactor to improve pollutants removal and a periphyton bioreactor with an 84 cm column was built to investigate microbe-wastewater interactions. Periphyton greatly improved water quality and produced a distinct stratification in the water column into five redox zones with slight overlaps. From top to bottom these were: oxygen reduction, nitrate reduction, iron reduction, sulfate reduction and methanogenic zone. Periphyton communities had high species diversities (767-947 OTUs) with the facultative zone (middle layer) having higher species richness and functional diversity than the aerobic (top layer) and anaerobic zones (bottom layer). A good knowledge of interactions between periphyton and water column stratification could benefit from integration of periphyton to improve bioremediation of deep and static water.
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Affiliation(s)
- Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Wei Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Fengwu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Philip Kerr
- School of Biomedical Sciences, Charles Sturt University, Boorooma St., Wagga Wagga, NSW 2678, Australia
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.
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743
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Zhang H, Wen Q, An Z, Chen Z, Nan J. Analysis of long-term performance and microbial community structure in bio-cathode microbial desalination cells. Environ Sci Pollut Res Int 2016; 23:5931-5940. [PMID: 26596826 DOI: 10.1007/s11356-015-5794-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
A microbial desalination cell (MDC) could desalinate salt water without energy consumption and simultaneously generate bioenergy. Compared with an abiotic cathode MDC, an aerobic bio-cathode MDC is more sustainable and is less expensive to operate. In this study, the long-term operation (5500 h) performance of a bio-cathode MDC was investigated in which the power density, Coulombic efficiency, and salt removal rate were decreased by 71, 44, and 27 %, respectively. The primary reason for the system performance decrease was biofouling on the membranes, which increased internal resistance and reduced the ionic transfer and energy conversion efficiency. Changing membranes was an effective method to recover the MDC performance. The microbial community diversity in the MDC anode was low compared with that of the reported microbial fuel cell (MFC), while the abundance of Proteobacteria was 30 % higher. The content of Planctomycetes in the cathode biofilm sample was much higher than that in biofouling on the cation exchange membrane (CEM), indicating that Planctomycetes were relevant to cathode oxygen reduction.
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Affiliation(s)
- Huichao Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, People's Republic of China
- School of Civil Engineering, Yantai University, Yantai, 264000, People's Republic of China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, People's Republic of China
| | - Zhongyi An
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, People's Republic of China
- School of Civil Engineering, Yantai University, Yantai, 264000, People's Republic of China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, People's Republic of China.
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, People's Republic of China.
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, People's Republic of China
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744
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Kaci A, Petit F, Fournier M, Cécillon S, Boust D, Lesueur P, Berthe T. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core. Environ Sci Pollut Res Int 2016; 23:4095-4110. [PMID: 25934230 DOI: 10.1007/s11356-015-4506-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/06/2015] [Indexed: 06/04/2023]
Abstract
In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community.
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Affiliation(s)
- Assia Kaci
- Normandie Université, UR, UMR CNRS 6143 M2C, FED 4116, 76821, Mont Saint Aignan, France
| | - Fabienne Petit
- Normandie Université, UR, UMR CNRS 6143 M2C, FED 4116, 76821, Mont Saint Aignan, France
| | - Matthieu Fournier
- Normandie Université, UR, UMR CNRS 6143 M2C, FED 4116, 76821, Mont Saint Aignan, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Dominique Boust
- IRSN, Laboratoire de Radioécologie de Cherbourg-Octeville (LRC), 50130, Cherbourg-Octeville, France
| | - Patrick Lesueur
- Normandie Université, UR, UMR CNRS 6143 M2C, FED 4116, 76821, Mont Saint Aignan, France
| | - Thierry Berthe
- Normandie Université, UR, UMR CNRS 6143 M2C, FED 4116, 76821, Mont Saint Aignan, France.
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745
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Rietl AJ, Overlander ME, Nyman AJ, Jackson CR. Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes. Microb Ecol 2016; 71:290-303. [PMID: 26271740 DOI: 10.1007/s00248-015-0651-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/14/2015] [Indexed: 06/04/2023]
Abstract
Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors such as salinity that control plant zonation in saltmarshes are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA. All three systems exhibit a patchy distribution of Juncus roemerianus stands within a Spartina alterniflora marsh. Sediment samples were collected from the interior of several J. roemerianus stands as well as from the S. alterniflora matrix. Samples were assayed for extracellular enzyme activity and DNA extracted to determine microbial community composition. Denaturing gradient gel electrophoresis of rRNA gene fragments was used to determine regional patterns in bacterial, archaeal, and fungal assemblages, while Illumina sequencing was used to examine local, vegetation-driven, patterns in community structure at one site. Both enzyme activity and microbial community structure were primarily influenced by regional site. Within individual saltmarshes, bacterial and archaeal communities differed between J. roemerianus and S. alterniflora vegetated sediments, while fungal communities did not. These results highlight the importance of the plant community in shaping the sediment microbial community in saltmarshes but also demonstrate that regional scale factors are at least as important.
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Affiliation(s)
- Anthony J Rietl
- School of Renewable Natural Resources, Renewable Natural Resources Department, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Megan E Overlander
- Department of Biology, The University of Mississippi, Shoemaker Hall, Oxford, MS, 38677, USA
| | - Andrew J Nyman
- School of Renewable Natural Resources, Renewable Natural Resources Department, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Colin R Jackson
- Department of Biology, The University of Mississippi, Shoemaker Hall, Oxford, MS, 38677, USA
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746
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Abstract
Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures' emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes.
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Affiliation(s)
- Chun-Huo Chiu
- Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan
| | - Anne Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan
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747
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Gannoun H, Omri I, Chouari R, Khelifi E, Keskes S, Godon JJ, Hamdi M, Sghir A, Bouallagui H. Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters. Bioresour Technol 2016; 201:337-346. [PMID: 26687494 DOI: 10.1016/j.biortech.2015.11.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge.
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Affiliation(s)
- Hana Gannoun
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia; Université de Tunis El Manar, ISSBAT, 9, Avenue Zouhaïer Essafi, 1006 Tunis, Tunisia
| | - Ilhem Omri
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | - Rakia Chouari
- Faculté des Sciences de Bizerte, Unité de Toxicologie Végétale et Biologie moléculaire des micro-organismes (UR11-ES-32), Tunisia
| | - Eltaief Khelifi
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | - Sajiaa Keskes
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | | | - Moktar Hamdi
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | - Abdelghani Sghir
- Université d'Evry Val d'Essonne (UEVE), Evry, France; CEA, Institut de Génomique, Genoscope, Evry, France
| | - Hassib Bouallagui
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia.
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748
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Benítez-Páez A, Portune KJ, Sanz Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer. Gigascience 2016; 5:4. [PMID: 26823973 PMCID: PMC4730766 DOI: 10.1186/s13742-016-0111-z] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/12/2016] [Indexed: 01/17/2023] Open
Abstract
Background The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION™ system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences. Results Using R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. These data were sufficient to reconstruct more than 90 % of the 16S rRNA gene sequences for 20 different species present in a mock reference community. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to assign taxonomic classification down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using ‘universal’ primers. Conclusions Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, the MinION™ DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements in nanopore chemistry, such as minimising base-calling errors and the nucleotide bias reported here for 16S amplicon sequencing, will further deliver more reliable information that is useful for the specific detection of microbial species and strains in complex ecosystems.
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Affiliation(s)
- Alfonso Benítez-Páez
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology Institute, Spanish National Research Council (IATA-CSIC), C. Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia Spain
| | - Kevin J Portune
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology Institute, Spanish National Research Council (IATA-CSIC), C. Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology Institute, Spanish National Research Council (IATA-CSIC), C. Catedràtic Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia Spain
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749
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Chen J, Ryu E, Hathcock M, Ballman K, Chia N, Olson JE, Nelson H. Impact of demographics on human gut microbial diversity in a US Midwest population. PeerJ 2016; 4:e1514. [PMID: 26839739 PMCID: PMC4734456 DOI: 10.7717/peerj.1514] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/21/2022] Open
Abstract
The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior-related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies.
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Affiliation(s)
- Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota , United States
| | - Matthew Hathcock
- Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota , United States
| | - Karla Ballman
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States; Division of Biostatistics and Epidemiology, Weill Medical College of Cornell University, New York, New York, United States
| | - Nicholas Chia
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States; Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota , United States
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States; Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States
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750
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Abdallah MB, Karray F, Mhiri N, Mei N, Quéméneur M, Cayol JL, Erauso G, Tholozan JL, Alazard D, Sayadi S. Prokaryotic diversity in a Tunisian hypersaline lake, Chott El Jerid. Extremophiles 2016; 20:125-38. [PMID: 26724953 DOI: 10.1007/s00792-015-0805-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/06/2015] [Indexed: 11/30/2022]
Abstract
Prokaryotic diversity was investigated in a Tunisian salt lake, Chott El Jerid, by quantitative real-time PCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting methods targeting the 16S rRNA gene and culture-dependent methods. Two different samples S1-10 and S2-10 were taken from under the salt crust of Chott El Jerid in the dry season. DGGE analysis revealed that bacterial sequences were related to Firmicutes, Proteobacteria, unclassified bacteria, and Deinococcus-Thermus phyla. Anaerobic fermentative and sulfate-reducing bacteria were also detected in this ecosystem. Within the domain archaea, all sequences were affiliated to Euryarchaeota phylum. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of bacteria was 5 × 10(6) DNA copies g(-1) whereas archaea varied between 5 × 10(5) and 10(6) DNA copies g(-1) in these samples. Eight anaerobic halophilic fermentative bacterial strains were isolated and affiliated with the species Halanaerobium alcaliphilum, Halanaerobium saccharolyticum, and Sporohalobacter salinus. These data showed an abundant and diverse microbial community detected in the hypersaline thalassohaline environment of Chott El Jerid.
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Affiliation(s)
- Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia. .,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia.
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
| | - Nan Mei
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Marianne Quéméneur
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Jean-Luc Cayol
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Gaël Erauso
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
| | - Jean-Luc Tholozan
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Didier Alazard
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
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