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Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
- *Correspondence: Josefa Antón,
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2
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Jordan D, Mills D. Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.646130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.
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3
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Jung J, Gillevet PM, Sikaroodi M, Andrews J, Song B, Shields JD. Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus. DISEASES OF AQUATIC ORGANISMS 2021; 143:147-158. [PMID: 33629659 DOI: 10.3354/dao03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.
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Affiliation(s)
- Jibom Jung
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
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4
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Johnston‐Monje D, Lopez Mejia J. Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11334. [PMID: 32351795 PMCID: PMC7186905 DOI: 10.1002/aps3.11334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/28/2020] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.
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Affiliation(s)
- David Johnston‐Monje
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
- Max Planck Institute for Plant Breeding ResearchDepartment of Plant Microbe InteractionsCarl-von-Linne-Weg 10D-50829CologneGermany
| | - Jessica Lopez Mejia
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
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5
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Hewson I. Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson. DISEASES OF AQUATIC ORGANISMS 2019; 137:109-124. [PMID: 31854329 DOI: 10.3354/dao03432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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6
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Zhou JL, Xu J, Jiao AG, Yang L, Chen J, Callac P, Liu Y, Wang SX. Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom. Front Microbiol 2019; 10:2686. [PMID: 31803173 PMCID: PMC6877668 DOI: 10.3389/fmicb.2019.02686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022] Open
Abstract
The polymerase chain reaction (PCR) is widely used in modern biology and medicine. However, PCR artifacts can complicate the interpretation of PCR-based results. The internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster is the consensus fungal barcode marker and suspected PCR artifacts have been reported in many studies, especially for the analyses of environmental fungal samples. At present, the patterns of PCR artifacts in the whole fungal ITS region (ITS1+5.8S+ITS2) are not known. In this study, we analyzed the error rates of PCR at three template complexity levels using the divergent copies of ITS from the mushroom Agaricus subrufescens. Our results showed that PCR using the Phusion® High-Fidelity DNA Polymerase has a per nucleotide error rate of about 4 × 10–6 per replication. Among the detected mutations, transitions were much more frequent than transversions, insertions, and deletions. When divergent alleles were mixed as templates in the same reaction, a significant proportion (∼30%) of recombinant molecules were detected. The in vitro mixed-template results were comparable to those obtained from using the genomic DNA of the original mushroom specimen as template. Our results indicate that caution should be in place when interpreting ITS sequences from individual fungal specimens, especially those containing divergent ITS copies. Similar results could also happen to PCR-based analyses of other multicopy DNA fragments as well as single-copy DNA sequences with divergent alleles in diploid organisms.
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Affiliation(s)
- Jun-Liang Zhou
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China.,International Exchange and Cooperation Department, Kunming University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - An-Guo Jiao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Li Yang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Jie Chen
- Instituto de Ecología, Veracruz, Mexico
| | | | - Yu Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Shou-Xian Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
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7
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Antibacterial activity and lantibiotic post-translational modification genes in Streptococcus spp. isolated from ruminal fluid. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1407-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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8
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Savo Sardaro ML, Perin LM, Bancalari E, Neviani E, Gatti M. Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods. Food Microbiol 2018; 74:113-119. [PMID: 29706326 DOI: 10.1016/j.fm.2018.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/31/2022]
Abstract
The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.
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Affiliation(s)
- Maria Luisa Savo Sardaro
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy; San Raffaele University, Department of Nutrition and Gastronomy, Via Val Cannuta 247, Rome, Italy.
| | - Luana Martins Perin
- Universidade Federal de Viçosa, Departamento de Veterinaria, Campus Universitario, Centro, 36570-900 Viçosa, MG, Brazil
| | - Elena Bancalari
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Erasmo Neviani
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Monica Gatti
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
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9
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Leight AK, Crump BC, Hood RR. Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area. Front Microbiol 2018; 9:384. [PMID: 29593669 PMCID: PMC5861211 DOI: 10.3389/fmicb.2018.00384] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/20/2018] [Indexed: 01/04/2023] Open
Abstract
Routine monitoring of shellfish growing waters for bacteria indicative of human sewage pollution reveals little about the bacterial communities that co-occur with these indicators. This study investigated the bacterial community, potential pathogens, and fecal indicator bacteria in 40 water samples from a shellfish growing area in the Chesapeake Bay, USA. Bacterial community composition was quantified with deep sequencing of 16S rRNA gene amplicons, and absolute gene abundances were estimated with an internal standard (Thermus thermophilus genomes). Fecal coliforms were quantified by culture, and Vibrio vulnificus and V. parahaemolyticus with quantitative PCR. Fecal coliforms and V. vulnificus were detected in most samples, and a diverse assemblage of potential human pathogens were detected in all samples. These taxa followed two general patterns of abundance. Fecal coliforms and 16S rRNA genes for Enterobacteriaceae, Aeromonas, Arcobacter, Staphylococcus, and Bacteroides increased in abundance after a 1.3-inch rain event in May, and, for some taxa, after smaller rain events later in the season, suggesting that these are allochthonous organisms washed in from land. Clostridiaceae and Mycobacterium 16S rRNA gene abundances increased with day of the year and were not positively related to rainfall, suggesting that these are autochthonous organisms. Other groups followed both patterns, such as Legionella. Fecal coliform abundance did not correlate with most other taxa, but were extremely high following the large rainstorm in May when they co-occurred with a broad range of potential pathogen groups. V. vulnificus were absent during the large rainstorm, and did not correlate with 16S rRNA abundances of Vibrio spp. or most other taxa. These results highlight the complex nature of bacterial communities and the limited utility of using specific bacterial groups as indicators of pathogen presence.
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Affiliation(s)
- Andrew K Leight
- Cooperative Oxford Laboratory, National Ocean Service/National Centers for Coastal Ocean Science, National Oceanic and Atmospheric Administration (NOAA), Oxford, MD, United States.,Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Raleigh R Hood
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States
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10
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Damaso N, Mendel J, Mendoza M, von Wettberg EJ, Narasimhan G, Mills D. Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance. J Forensic Sci 2018; 63:1033-1042. [PMID: 29357400 DOI: 10.1111/1556-4029.13741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 01/23/2023]
Abstract
Soil DNA profiling has potential as a forensic tool to establish a link between soil collected at a crime scene and soil recovered from a suspect. However, a quantitative measure is needed to investigate the spatial/temporal variability across multiple scales prior to their application in forensic science. In this study, soil DNA profiles across Miami-Dade, FL, were generated using length heterogeneity PCR to target four taxa. The objectives of this study were to (i) assess the biogeographical patterns of soils to determine whether soil biota is spatially correlated with geographic location and (ii) evaluate five machine learning algorithms for their predictive ability to recognize biotic patterns which could accurately classify soils at different spatial scales regardless of seasonal collection. Results demonstrate that soil communities have unique patterns and are spatially autocorrelated. Bioinformatic algorithms could accurately classify soils across all scales with Random Forest significantly outperforming all other algorithms regardless of spatial level.
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Affiliation(s)
- Natalie Damaso
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Julian Mendel
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Maria Mendoza
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Eric J von Wettberg
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Center for Tropical Botany, Florida International University, 4013 South Douglas Road, Miami, FL 33133
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
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11
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Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR. Int J Food Microbiol 2017; 242:24-36. [DOI: 10.1016/j.ijfoodmicro.2016.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/08/2016] [Accepted: 11/09/2016] [Indexed: 12/27/2022]
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12
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Torzilli AP, Sikaroodi M, Chalkley D, Gillevet PM. A comparison of fungal communities from four salt marsh plants using automated ribosomal intergenic spacer analysis (ARISA). Mycologia 2017. [DOI: 10.1080/15572536.2006.11832641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Albert P. Torzilli
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia 22030
| | - Masoumeh Sikaroodi
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia 20110
| | - David Chalkley
- American Type Culture Collection, 10801 University Boulevard, Manassas, Virginia 20110-2209
| | - Patrick M. Gillevet
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia 20110
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13
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Methylophilaceae and Hyphomicrobium as target taxonomic groups in monitoring the function of methanol-fed denitrification biofilters in municipal wastewater treatment plants. ACTA ACUST UNITED AC 2017; 44:35-47. [DOI: 10.1007/s10295-016-1860-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/30/2016] [Indexed: 01/05/2023]
Abstract
Abstract
Molecular monitoring of bacterial communities can explain and predict the stability of bioprocesses in varying physicochemical conditions. To study methanol-fed denitrification biofilters of municipal wastewater treatment plants, bacterial communities of two full-scale biofilters were compared through fingerprinting and sequencing of the 16S rRNA genes. Additionally, 16S rRNA gene fingerprinting was used for 10-week temporal monitoring of the bacterial community in one of the biofilters. Combining the data with previous study results, the family Methylophilaceae and genus Hyphomicrobium were determined as suitable target groups for monitoring. An increase in the relative abundance of Hyphomicrobium-related biomarkers occurred simultaneously with increases in water flow, NOx − load, and methanol addition, as well as a higher denitrification rate, although the dominating biomarkers linked to Methylophilaceae showed an opposite pattern. The results indicate that during increased loading, stability of the bioprocess is maintained by selection of more efficient denitrifier populations, and this progress can be analyzed using simple molecular fingerprinting.
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14
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Can the development and autolysis of lactic acid bacteria influence the cheese volatile fraction? The case of Grana Padano. Int J Food Microbiol 2016; 233:20-28. [DOI: 10.1016/j.ijfoodmicro.2016.06.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/23/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022]
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15
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Giner CR, Forn I, Romac S, Logares R, de Vargas C, Massana R. Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes. Appl Environ Microbiol 2016; 82:4757-4766. [PMID: 27235440 PMCID: PMC4984273 DOI: 10.1128/aem.00560-16] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescence in situ hybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances. IMPORTANCE Direct studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescence in situ hybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.
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Affiliation(s)
- Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Université Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Université Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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16
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Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C, Albanese D, Corvaglia LT, Faldella G, Di Gioia D. Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions. Appl Microbiol Biotechnol 2016; 100:5537-46. [PMID: 26971496 DOI: 10.1007/s00253-016-7410-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 02/04/2023]
Abstract
Different factors are known to influence the early gut colonization in newborns, among them the perinatal use of antibiotics. On the other hand, the effect on the baby of the administration of antibiotics to the mother during labor, referred to as intrapartum antibiotic prophylaxis (IAP), has received less attention, although routinely used in group B Streptococcus positive women to prevent the infection in newborns. In this work, the fecal microbiota of neonates born to mothers receiving IAP and of control subjects were compared taking advantage for the first time of high-throughput DNA sequencing technology. Seven different 16S rDNA hypervariable regions (V2, V3, V4, V6 + V7, V8, and V9) were amplified and sequenced using the Ion Torrent Personal Genome Machine. The results obtained showed significant differences in the microbial composition of newborns born to mothers who had received IAP, with a lower abundance of Actinobacteria and Bacteroidetes as well as an overrepresentation of Proteobacteria. Considering that the seven hypervariable regions showed different discriminant ability in the taxonomic identification, further analyses were performed on the V4 region evidencing in IAP infants a reduced microbial richness and biodiversity, as well as a lower number of bacterial families with a predominance of Enterobacteriaceae members. In addition, this analysis pointed out a significant reduction in Bifidobacterium spp. strains. The reduced abundance of these beneficial microorganisms, together with the increased amount of potentially pathogenic bacteria, may suggest that IAP infants are more exposed to gastrointestinal or generally health disorders later in age.
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Affiliation(s)
- Irene Aloisio
- Department of Agricultural Sciences, University of Bologna, viale Fanin 42, 40127, Bologna, Italy
| | - Andrea Quagliariello
- Laboratory of Molecular Anthropology, Centre for Genome Biology Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology, Centre for Genome Biology Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Centre for Genome Biology Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Carlotta De Filippo
- Institute of Biometeorology (IBIMET), National Research Council (CNR), Via G. Caproni 8, 50145, Florence, Italy
| | - Davide Albanese
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Luigi Tommaso Corvaglia
- Neonatal Intensive Care Unit, S. Orsola Malpighi Hospital, Via Massarenti 11, 40138, Bologna, Italy
| | - Giacomo Faldella
- Neonatal Intensive Care Unit, S. Orsola Malpighi Hospital, Via Massarenti 11, 40138, Bologna, Italy
| | - Diana Di Gioia
- Department of Agricultural Sciences, University of Bologna, viale Fanin 42, 40127, Bologna, Italy.
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17
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Read DS, Matzke M, Gweon HS, Newbold LK, Heggelund L, Ortiz MD, Lahive E, Spurgeon D, Svendsen C. Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4120-4128. [PMID: 25903189 DOI: 10.1007/s11356-015-4538-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/12/2015] [Indexed: 06/04/2023]
Abstract
Zinc oxide nanoparticles (ZnO NPs) are used in an array of products and processes, ranging from personal care products to antifouling paints, textiles, food additives, antibacterial agents and environmental remediation processes. Soils are an environment likely to be exposed to manmade nanoparticles due to the practice of applying sewage sludge as a fertiliser or as an organic soil improver. However, understanding on the interactions between soil properties, nanoparticles and the organisms that live within soil is lacking, especially with regards to soil bacterial communities. We studied the effects of nanoparticulate, non-nanoparticulate and ionic zinc (in the form of zinc chloride) on the composition of bacterial communities in soil with a modified pH range (from pH 4.5 to pH 7.2). We observed strong pH-dependent effects on the interaction between bacterial communities and all forms of zinc, with the largest changes in bacterial community composition occurring in soils with low and medium pH levels (pH 4.8 and 5.9). The high pH soil (pH 7.2) was less susceptible to the effects of zinc exposure. At the highest doses of zinc (2500 mg/kg dw soil), both nano and non-nano particulate zinc applications elicited a similar response in the soil bacterial community, and this differed significantly to the ionic zinc salt treatment. The results highlight the importance of considering soil pH in nanotoxicology studies, although further work is needed to determine the exact mechanisms controlling the toxicity and fate and interactions of nanoparticles with soil microbial communities.
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Affiliation(s)
- Daniel S Read
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK.
| | - Marianne Matzke
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Hyun S Gweon
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Lindsay K Newbold
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Laura Heggelund
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, building 113, 2800, Kgs Lyngby, Denmark
| | - Maria Diez Ortiz
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
- LEITAT Technological Center, C/ de la Innovació, 2, 08225, Terrassa, Barcelona, Spain
| | - Elma Lahive
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - David Spurgeon
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Claus Svendsen
- NERC Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
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18
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Yan L, Sinkko H, Penttinen P, Lindström K. Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 542:817-25. [PMID: 26556745 DOI: 10.1016/j.scitotenv.2015.10.144] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 05/20/2023]
Abstract
The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ.
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Affiliation(s)
- Lijuan Yan
- Department of Environmental Sciences, PO Box 65 (Viikinkaari 2a), 00014, University of Helsinki, Finland.
| | - Hanna Sinkko
- Department of Food and Environmental Sciences, PO Box 56 (Latokartanonkaari 11), 00014, University of Helsinki, Finland
| | - Petri Penttinen
- Department of Environmental Sciences, PO Box 65 (Viikinkaari 2a), 00014, University of Helsinki, Finland
| | - Kristina Lindström
- Department of Environmental Sciences, PO Box 65 (Viikinkaari 2a), 00014, University of Helsinki, Finland
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19
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Herbold CW, Pelikan C, Kuzyk O, Hausmann B, Angel R, Berry D, Loy A. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front Microbiol 2015; 6:731. [PMID: 26236305 PMCID: PMC4503924 DOI: 10.3389/fmicb.2015.00731] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/03/2015] [Indexed: 12/11/2022] Open
Abstract
High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology.
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Affiliation(s)
| | | | | | | | | | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of ViennaVienna, Austria
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20
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Almeida-Dalmet S, Sikaroodi M, Gillevet PM, Litchfield CD, Baxter BK. Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. Microorganisms 2015; 3:310-26. [PMID: 27682091 PMCID: PMC5023243 DOI: 10.3390/microorganisms3030310] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 01/18/2023] Open
Abstract
We employed a temporal sampling approach to understand how the microbial diversity may shift in the north arm of Great Salt Lake, Utah, U.S. To determine how variations in seasonal environmental factors affect microbial communities, length heterogeneity PCR fingerprinting was performed using consensus primers for the domain Bacteria, and the haloarchaea. The archaeal fingerprints showed similarities during 2003 and 2004, but this diversity changed during the remaining two years of the study, 2005 and 2006. We also performed molecular phylogenetic analysis of the 16S rRNA genes of the whole microbial community to characterize the taxa in the samples. Our results indicated that in the domain, Bacteria, the Salinibacter group dominated the populations in all samplings. However, in the case of Archaea, as noted by LIBSHUFF for phylogenetic relatedness analysis, many of the temporal communities were distinct from each other, and changes in community composition did not track with environmental parameters. Around 20-23 different phylotypes, as revealed by rarefaction, predominated at different periods of the year. Some phylotypes, such as Haloquadradum, were present year-round although they changed in their abundance in different samplings, which may indicate that these species are affected by biotic factors, such as nutrients or viruses, that are independent of seasonal temperature dynamics.
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Affiliation(s)
- Swati Almeida-Dalmet
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA.
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA.
| | - Patrick M Gillevet
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA.
| | - Carol D Litchfield
- Microbiome Analysis Center, Department of Environmental Science and Policy, George Mason University, 10900 University Blvd., Manassas, VA 20110, USA.
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT 84105, USA.
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21
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Vannini C, Volpi M, Lardicci C. A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin? PLoS One 2015; 10:e0129942. [PMID: 26075405 PMCID: PMC4468208 DOI: 10.1371/journal.pone.0129942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
Organism body size has been demonstrated to be a discriminating element in shaping the response of living beings to environmental factors, thus playing a fundamental role in community structuring. Despite the importance of studies elucidating relations among communities of different size levels in ecosystems, the attempts that have been made in this sense are still very scarce and a reliable approach for these research still has to be defined. We characterized the benthic communities of bacteria, microbial eukaryotes, meiofauna and macrofauna in a coastal environment, encompassing a 10000-fold gradient in body size, testing and discussing a mixed approach of molecular fingerprinting for microbes and morphological observations for meio- and macrofauna. We found no correlation among structures of the different size-level communities: this suggests that community composition at one size-level could have no (or very low) influence on the community composition at other size-levels. Moreover, each community responds in a different way to the environmental parameters and with a degree of sensitivity which seems to increase with organism size. Therefore, our data indicate that the characterization of all the different size levels is clearly a necessity in order to study the dynamics really acting in a system.
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Affiliation(s)
- Claudia Vannini
- Department of Biology, University of Pisa, Pisa, Italy
- * E-mail:
| | - Marta Volpi
- Department of Biology, University of Pisa, Pisa, Italy
- Center for Geomicrobiology, Institute of Bioscience, University of Aarhus, Aarhus, Denmark
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22
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Rock C, Rivera B, Gerba CP. Microbial Source Tracking. Environ Microbiol 2015. [DOI: 10.1016/b978-0-12-394626-3.00014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Abstract
The increasing interest towards cellular heterogeneity within cell populations has pushed the development of new protocols to isolate and analyze single cells. PCR-based amplification techniques are widely used in this field. However, setting up an experiment and analyzing the results can sometimes be challenging. The aim of this chapter is to provide a general overview on single-cell PCR analysis focusing on the potential pitfalls and on the possible solutions to successfully perform the analysis.
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Chiquette J, Lagrost J, Girard C, Talbot G, Li S, Plaizier J, Hindrichsen I. Efficacy of the direct-fed microbial Enterococcus faecium alone or in combination with Saccharomyces cerevisiae or Lactococcus lactis during induced subacute ruminal acidosis. J Dairy Sci 2015; 98:190-203. [DOI: 10.3168/jds.2014-8219] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022]
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25
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Oliver AE, Newbold LK, Whiteley AS, van der Gast CJ. Marine bacterial communities are resistant to elevated carbon dioxide levels. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:574-582. [PMID: 25756110 DOI: 10.1111/1758-2229.12159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification.
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26
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Mikkonen A, Santalahti M, Lappi K, Pulkkinen AM, Montonen L, Suominen L. Bacterial and archaeal communities in long-term contaminated surface and subsurface soil evaluated through coextracted RNA and DNA. FEMS Microbiol Ecol 2014; 90:103-14. [PMID: 24986450 DOI: 10.1111/1574-6941.12376] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 06/10/2014] [Accepted: 06/25/2014] [Indexed: 11/28/2022] Open
Abstract
Soil RNA and DNA were coextracted along a contamination gradient at a landfarming field with aged crude oil contamination to investigate pollution-dependent differences in 16S rRNA and rRNA gene pools. Microbial biomass correlated with nucleic acid yields as well as bacterial community change, indicating that the same factors controlled community size and structure. In surface soil, bacterial community evenness, estimated through length heterogeneity PCR (LH-PCR) fingerprinting, appeared higher for RNA-based than for DNA-based communities. The RNA-based community profiles resembled the DNA-based communities of soil with a lower contamination level. Cloning-based identification of bacterial hydrocarbon-degrading taxa in the RNA pool, representing the viable community with high protein synthesis potential, indicated that decontamination processes still continue. Analyses of archaea revealed that only Thaumarchaeota were present in the aerobic samples, whereas more diverse communities were found in the compacted subsurface soil with more crude oil. For subsurface bacteria, hydrocarbon concentration explained neither the community structure nor the difference between RNA-based and DNA-based communities. However, rRNA of bacterial taxa associated with syntrophic and sulphate-reducing alkane degradation was detected. Although the same prokaryotic taxa were identified in DNA and RNA, comparison of the two nucleic acid pools can aid in the assessment of past and future restoration success.
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Affiliation(s)
- Anu Mikkonen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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27
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Sagarkar S, Nousiainen A, Shaligram S, Björklöf K, Lindström K, Jørgensen KS, Kapley A. Soil mesocosm studies on atrazine bioremediation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2014; 139:208-216. [PMID: 24721596 DOI: 10.1016/j.jenvman.2014.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 06/03/2023]
Abstract
Accumulation of pesticides in the environment causes serious issues of contamination and toxicity. Bioremediation is an ecologically sound method to manage soil pollution, but the bottleneck here, is the successful scale-up of lab-scale experiments to field applications. This study demonstrates pilot-scale bioremediation in tropical soil using atrazine as model pollutant. Mimicking field conditions, three different bioremediation strategies for atrazine degradation were explored. 100 kg soil mesocosms were set-up, with or without atrazine application history. Natural attenuation and enhanced bioremediation were tested, where augmentation with an atrazine degrading consortium demonstrated best pollutant removal. 90% atrazine degradation was observed in six days in soil previously exposed to atrazine, while soil without history of atrazine use, needed 15 days to remove the same amount of amended atrazine. The bacterial consortium comprised of 3 novel bacterial strains with different genetic atrazine degrading potential. The progress of bioremediation was monitored by measuring the levels of atrazine and its intermediate, cyanuric acid. Genes from the atrazine degradation pathway, namely, atzA, atzB, atzD, trzN and trzD were quantified in all mesocosms for 60 days. The highest abundance of all target genes was observed on the 6th day of treatment. trzD was observed in the bioaugmented mesocosms only. The bacterial community profile in all mesocosms was monitored by LH-PCR over a period of two months. Results indicate that the communities changed rapidly after inoculation, but there was no drastic change in microbial community profile after 1 month. Results indicated that efficient bioremediation of atrazine using a microbial consortium could be successfully up-scaled to pilot scale.
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Affiliation(s)
- Sneha Sagarkar
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India
| | - Aura Nousiainen
- Finnish Environment Institute, PO Box 140, FI-00251 Helsinki, Finland
| | - Shraddha Shaligram
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India
| | - Katarina Björklöf
- Finnish Environment Institute, PO Box 140, FI-00251 Helsinki, Finland
| | - Kristina Lindström
- Department of Food and Environmental Sciences, Division of Microbiology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Atya Kapley
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India.
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28
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Ibarbalz FM, Pérez MV, Figuerola ELM, Erijman L. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics. PLoS One 2014; 9:e99722. [PMID: 24923665 PMCID: PMC4055690 DOI: 10.1371/journal.pone.0099722] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/19/2014] [Indexed: 11/19/2022] Open
Abstract
The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.
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Affiliation(s)
- Federico M. Ibarbalz
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - María Victoria Pérez
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
- Agua y Saneamientos Argentinos S.A. (AySA), Buenos Aires, Argentina
| | - Eva L. M. Figuerola
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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29
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Masse L, Mondor M, Talbot G, Deschênes L, Drolet H, Gagnon N, St-Germain F, Puig-Bargués J. Fouling of Reverse Osmosis Membranes Processing Swine Wastewater Pretreated by Mechanical Separation and Aerobic Biofiltration. SEP SCI TECHNOL 2014. [DOI: 10.1080/01496395.2014.881880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Bao QL, Xiao KQ, Chen Z, Yao HY, Zhu YG. Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw. FEMS Microbiol Ecol 2014; 88:372-85. [DOI: 10.1111/1574-6941.12305] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 11/25/2022] Open
Affiliation(s)
- Qiong-Li Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Ke-Qing Xiao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Zheng Chen
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Huai-Ying Yao
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
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31
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Joo S, Han D, Lee EJ, Park S. Use of length heterogeneity polymerase chain reaction (LH-PCR) as non-invasive approach for dietary analysis of Svalbard reindeer, Rangifer tarandus platyrhynchus. PLoS One 2014; 9:e91552. [PMID: 24618847 PMCID: PMC3950246 DOI: 10.1371/journal.pone.0091552] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 02/13/2014] [Indexed: 11/25/2022] Open
Abstract
To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.
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Affiliation(s)
- Sungbae Joo
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - Donguk Han
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Eun Ju Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Sangkyu Park
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- * E-mail:
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Santarelli M, Bottari B, Lazzi C, Neviani E, Gatti M. Survey on the community and dynamics of lactic acid bacteria in Grana Padano cheese. Syst Appl Microbiol 2013; 36:593-600. [DOI: 10.1016/j.syapm.2013.04.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/16/2013] [Indexed: 10/26/2022]
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Pochon X, Bott NJ, Smith KF, Wood SA. Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS One 2013; 8:e73935. [PMID: 24023913 PMCID: PMC3762713 DOI: 10.1371/journal.pone.0073935] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/30/2013] [Indexed: 11/19/2022] Open
Abstract
Most surveillance programmes for marine invasive species (MIS) require considerable taxonomic expertise, are laborious, and are unable to identify species at larval or juvenile stages. Therefore, marine pests may go undetected at the initial stages of incursions when population densities are low. In this study, we evaluated the ability of the benchtop GS Junior™ 454 pyrosequencing system to detect the presence of MIS in complex sample matrices. An initial in-silico evaluation of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear small subunit ribosomal DNA (SSU) genes, found that multiple primer sets (targeting a ca. 400 base pair region) would be required to obtain species level identification within the COI gene. In contrast a single universal primer set was designed to target the V1-V3 region of SSU, allowing simultaneous PCR amplification of a wide taxonomic range of MIS. To evaluate the limits of detection of this method, artificial contrived communities (10 species from 5 taxonomic groups) were created using varying concentrations of known DNA samples and PCR products. Environmental samples (water and sediment) spiked with one or five 160 hr old Asterias amurensis larvae were also examined. Pyrosequencing was able to recover DNA/PCR products of individual species present at greater than 0.64% abundance from all tested contrived communities. Additionally, single A. amurensis larvae were detected from both water and sediment samples despite the co-occurrence of a large array of environmental eukaryotes, indicating an equivalent sensitivity to quantitative PCR. NGS technology has tremendous potential for the early detection of marine invasive species worldwide.
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Affiliation(s)
- Xavier Pochon
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
- * E-mail:
| | - Nathan J. Bott
- Aquatic Sciences, South Australian Research and Development Institute, Adelaide, Australia
| | - Kirsty F. Smith
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
- School of Biological Sciences, University of Waikato, Hamilton, New Zealand
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Sorensen JPR, Maurice L, Edwards FK, Lapworth DJ, Read DS, Allen D, Butcher AS, Newbold LK, Townsend BR, Williams PJ. Using boreholes as windows into groundwater ecosystems. PLoS One 2013; 8:e70264. [PMID: 23936176 PMCID: PMC3729555 DOI: 10.1371/journal.pone.0070264] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 06/20/2013] [Indexed: 11/24/2022] Open
Abstract
Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m3 at 0.4–1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.
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Affiliation(s)
| | - Louise Maurice
- British Geological Survey, Wallingford, Oxon, United Kingdom
| | | | | | - Daniel S. Read
- Centre for Ecology and Hydrology, Wallingford, Oxon, United Kingdom
| | - Debbie Allen
- British Geological Survey, Wallingford, Oxon, United Kingdom
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Watanarojanaporn N, Longtonglang A, Boonkerd N, Tittabutr P, Lee J, Teaumroong N. Biases for detecting arbuscular mycorrhizal fungal mixture by terminal restriction fragment length polymorphism (T-RFLP). World J Microbiol Biotechnol 2013; 30:77-86. [DOI: 10.1007/s11274-013-1423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/28/2013] [Indexed: 11/28/2022]
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36
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Lettat A, Hassanat F, Benchaar C. Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities. J Dairy Sci 2013; 96:5237-48. [PMID: 23769352 DOI: 10.3168/jds.2012-6481] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/30/2013] [Indexed: 01/30/2023]
Abstract
Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable enough to reflect changes in ruminal methanogenesis. A more robust technique to characterize changes in archaeal community structures will help to better understand the microbial process involved in ruminal methanogenesis and, hence, enabling the development of more effective dietary CH4 mitigation strategies.
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Affiliation(s)
- A Lettat
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, Canada
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37
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Watanarojanaporn N, Boonkerd N, Tittabutr P, Longtonglang A, Young JPW, Teaumroong N. Effect of rice cultivation systems on indigenous arbuscular mycorrhizal fungal community structure. Microbes Environ 2013; 28:316-24. [PMID: 23719585 PMCID: PMC4070969 DOI: 10.1264/jsme2.me13011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/09/2013] [Indexed: 11/12/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) in an agricultural ecosystem are necessary for proper management of beneficial symbiosis. Here we explored how the patterns of the AMF community in rice roots were affected by rice cultivation systems (the system of rice intensification [SRI] and the conventional rice cultivation system [CS]), and by compost application during growth stages. Rice plants harvested from SRI-managed plots exhibited considerably higher total biomass, root dry weight, and seed fill than those obtained from conventionally managed plots. Our findings revealed that all AMF sequences observed from CS plots belonged (only) to the genus Glomus, colonizing in rice roots grown under this type of cultivation, while rice roots sown in SRI showed sequences belonging to both Glomus and Acaulospora. The AMF community was compared between the different cultivation types (CS and SRI) and compost applications by principle component analysis. In all rice growth stages, AMF assemblages of CS management were not separated from those of SRI management. The distribution of AMF community composition based on T-RFLP data showed that the AMF community structure was different among four cultivation systems, and there was a gradual increase of Shannon-Weaver indices of diversity (H') of the AMF community under SRI during growth stages. The results of this research indicated that rice grown in SRI-managed plots had more diverse AMF communities than those grown in CS plots.
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Affiliation(s)
- Nantida Watanarojanaporn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Aphakorn Longtonglang
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - J. Peter W. Young
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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38
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Sikaroodi M, Gillevet PM. Quality control in multi-tag pyrosequencing of microbial communities. Biotechniques 2013; 53:381-3. [PMID: 23227989 DOI: 10.2144/000113967] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 11/19/2012] [Indexed: 11/23/2022] Open
Abstract
Multi-tag pyrosequencing has become a key method in the analysis of microbial community composition. However, it is well known that kinetic bias during the initial PCR amplification of such microbial communities can dramatically distort amplicon abundance prior to downstream emulsion PCR and pyrosequencing. Here we present a simple protocol combining length-heterogeneity PCR fingerprinting with pyrosequencing to ensure the linearity of microbial community amplification. The method employs a fluorescently labeled reverse primer along with multi-tagged forward primers to initially amplify the microbial community. The resulting labeled amplicons are then fingerprinted, purified, and quantitated prior to emulsion PCR and pyrosequencing. Our data demonstrates: (i) use of this protocol results in a distribution of sequences showing linear amplification following emulsion PCR when compared with the initial length-heterogeneity PCR fingerprints, and (ii) that the added tags and labels do not have a negative effect on overall microbial community profiles.
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Affiliation(s)
- Masoumeh Sikaroodi
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia, USA.
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39
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Declercq AM, Haesebrouck F, Van den Broeck W, Bossier P, Decostere A. Columnaris disease in fish: a review with emphasis on bacterium-host interactions. Vet Res 2013; 44:27. [PMID: 23617544 PMCID: PMC3648355 DOI: 10.1186/1297-9716-44-27] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/10/2013] [Indexed: 11/10/2022] Open
Abstract
Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation.
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Affiliation(s)
- Annelies Maria Declercq
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Annemie Decostere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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40
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Lettat A, Benchaar C. Diet-induced alterations in total and metabolically active microbes within the rumen of dairy cows. PLoS One 2013; 8:e60978. [PMID: 23593365 PMCID: PMC3622600 DOI: 10.1371/journal.pone.0060978] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/05/2013] [Indexed: 12/13/2022] Open
Abstract
DNA-based techniques are widely used to study microbial populations; however, this approach is not specific to active microbes, because DNA may originate from inactive and/or dead cells. Using cDNA and DNA, respectively, we aimed to discriminate the active microbes from the total microbial community within the rumen of dairy cows fed diets with increasing proportions of corn silage (CS). Nine multiparous lactating Holstein cows fitted with ruminal cannulas were used in a replicated 3×3 Latin square (32-d period; 21-d adaptation) design to investigate diet-induced shifts in microbial populations by targeting the rDNA gene. Cows were fed a total mixed ration with the forage portion being either barley silage (0% CS), a 50∶50 mixture of barley silage and corn silage (50% CS), or corn silage (100% CS). No differences were found for total microbes analyzed by quantitative PCR, but changes were observed within the active ones. Feeding more CS to dairy cows was accompanied by an increase in Prevotella rRNA transcripts (P = 0.10) and a decrease in the protozoal rRNA transcripts (P<0.05). Although they were distributed differently among diets, 78% of the amplicons detected in DNA- and cDNA-based fingerprints were common to total and active bacterial communities. These may represent a bacterial core of abundant and active cells that drive the fermentation processes. In contrast, 10% of amplicons were specific to total bacteria and may represent inactive or dead cells, whereas 12% were only found within the active bacterial community and may constitute slow-growing bacteria with high metabolic activity. It appears that cDNA-based analysis is more discriminative to identify diet-induced shifts within the microbial community. This approach allows the detection of diet-induced changes in the microbial populations as well as particular bacterial amplicons that remained undetected using DNA-based methods.
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Affiliation(s)
- Abderzak Lettat
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Chaouki Benchaar
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, Canada
- * E-mail:
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41
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Neviani E, Bottari B, Lazzi C, Gatti M. New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano. Front Microbiol 2013; 4:36. [PMID: 23450500 PMCID: PMC3584316 DOI: 10.3389/fmicb.2013.00036] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/09/2013] [Indexed: 12/01/2022] Open
Abstract
Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the composition of microbial population changes under the influence of continuous shifts in environmental conditions and microorganisms interactions during manufacturing and ripening, the characteristics of a given cheese depend also on microflora dynamics. The microbiota present in cheese is complex and its growth and activity represent the most important, but the least controllable steps. In the past, research in this area was dependent on classical microbiological techniques. However, culture-dependent methods are time-consuming and approaches that include a culturing step can lead to inaccuracies due to species present in low numbers or simply uncultivable. Therefore, they cannot be used as a unique tool to monitor community dynamics. For these reasons approaches to cheese microbiology had to change dramatically. To address this, in recent years the focus on the use of culture-independent methods based on the direct analysis of DNA (or RNA) has rapidly increased. Application of such techniques to the study of cheese microbiology represents a rapid, sound, reliable, and effective way for the detection and identification of the microorganisms present in dairy products, leading to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality. In this article, an overview on the recent advances in the use of molecular methods for thorough analysis of microbial communities in cheeses is given. Furthermore, applications of culture-independent approaches to study the microbiology of two important raw-milk, long-ripened cheeses such as Grana Padano and Parmigiano Reggiano, are presented.
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Affiliation(s)
- Erasmo Neviani
- Department of Food Science, University of ParmaParma, Italy
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42
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Bottari B, Agrimonti C, Gatti M, Neviani E, Marmiroli N. Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters. Int J Food Microbiol 2012; 160:290-7. [PMID: 23290237 DOI: 10.1016/j.ijfoodmicro.2012.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/08/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of those species during ripening of derived dairy products. A major increase in understanding the starter culture contribution to cheese ecosystem could be harnessed to control cheese ripening and flavor formation.
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Affiliation(s)
- Benedetta Bottari
- Department of Food Science, University of Parma, Parco Area delle Scienze 95/A, Parma, Italy
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43
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Nishizawa T, Komatsuzaki M, Kaneko N, Ohta H. Archaeal Diversity of Upland Rice Field Soils Assessed by the Terminal Restriction Fragment Length Polymorphism Method Combined with Real Time Quantitative-PCR and a Clone Library Analysis. Microbes Environ 2012; 23:237-43. [PMID: 21558714 DOI: 10.1264/jsme2.23.237] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments.
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44
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Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 2012; 7:e44224. [PMID: 22970184 PMCID: PMC3435322 DOI: 10.1371/journal.pone.0044224] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 08/03/2012] [Indexed: 11/18/2022] Open
Abstract
Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.
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Affiliation(s)
- Charles K. Lee
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Craig W. Herbold
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - K. Eric Wommack
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America
| | | | - Ian R. McDonald
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America
- * E-mail:
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45
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Peura S, Eiler A, Hiltunen M, Nykänen H, Tiirola M, Jones RI. Bacterial and phytoplankton responses to nutrient amendments in a boreal lake differ according to season and to taxonomic resolution. PLoS One 2012; 7:e38552. [PMID: 22715392 PMCID: PMC3371014 DOI: 10.1371/journal.pone.0038552] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/11/2012] [Indexed: 11/18/2022] Open
Abstract
Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.
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Affiliation(s)
- Sari Peura
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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46
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Newbold LK, Oliver AE, Booth T, Tiwari B, DeSantis T, Maguire M, Andersen G, van der Gast CJ, Whiteley AS. The response of marine picoplankton to ocean acidification. Environ Microbiol 2012; 14:2293-307. [DOI: 10.1111/j.1462-2920.2012.02762.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Persistence and degrading activity of free and immobilised allochthonous bacteria during bioremediation of hydrocarbon-contaminated soils. Biodegradation 2012; 24:1-11. [PMID: 22555628 DOI: 10.1007/s10532-012-9553-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/23/2012] [Indexed: 11/27/2022]
Abstract
Rhodococcus sp. and Pseudomonas sp. bioremediation experiments were carried out using free and immobilized cells on natural carrier material (corncob powder) in order to evaluate the feasibility of its use in the bioremediation of hydrocarbon-contaminated soils. Terminal restriction fragment length polymorphism analysis was performed on the 16S rRNA gene as molecular fingerprinting method in order to assess the persistence of inoculated strains in the soil over time. Immobilized Pseudomonas cells degraded hydrocarbons more efficiently in the short term compared to the free ones. Immobilization seemed also to increase cell growth and stability in the soil. Free and immobilized Rhodococcus cells showed comparable degradation percentages, probably due to the peculiarity of Rhodococcus cells to aggregate into irregular clusters in the presence of hydrocarbons as sole carbon source. It is likely that the cells were not properly adsorbed on the porous matrix as a result of the small size of its pores. When Rhodococcus and Pseudomonas cells were co-immobilized on the matrix, a competition established between the two strains, that probably ended in the exclusion of Pseudomonas cells from the pores. The organic matrix might act as protective agent, but it also possibly limited cell density. Nevertheless, when the cells were properly adsorbed on the porous matrix, the immobilization became a suitable bioremediation strategy.
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Barret M, Gagnon N, Morissette B, Topp E, Kalmokoff M, Brooks SP, Matias F, Massé DI, Masse L, Talbot G. Methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks. FEMS Microbiol Ecol 2012; 80:427-40. [DOI: 10.1111/j.1574-6941.2012.01308.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/13/2011] [Accepted: 01/08/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Maialen Barret
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
| | - Nathalie Gagnon
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
| | - Bruno Morissette
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
| | - Edward Topp
- Southern Crop Protection and Food Research Centre; Agriculture and Agri-Food Canada; London; ON; Canada
| | - Martin Kalmokoff
- Atlantic Food and Horticulture Research Centre; Agriculture and Agri-Food Canada; Kentville; NS; Canada
| | - Stephen P.J. Brooks
- Bureau of Nutritional Sciences; Health Products and Foods Branch; Banting Research Centre; Ottawa; ON; Canada
| | - Fernando Matias
- Bureau of Nutritional Sciences; Health Products and Foods Branch; Banting Research Centre; Ottawa; ON; Canada
| | - Daniel I. Massé
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
| | - Lucie Masse
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
| | - Guylaine Talbot
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke; QC; Canada
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Tiao G, Lee CK, McDonald IR, Cowan DA, Cary SC. Rapid microbial response to the presence of an ancient relic in the Antarctic Dry Valleys. Nat Commun 2012; 3:660. [PMID: 22314356 DOI: 10.1038/ncomms1645] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/14/2011] [Indexed: 11/09/2022] Open
Abstract
The extreme cold and aridity of the Antarctic McMurdo Dry Valleys have led to the longstanding belief that metabolic rates of soil microbiota are negligible, and that ecosystem changes take place over millennia. Here we report the first direct experimental evidence that soil microbial communities undergo rapid and lasting changes in response to contemporary environmental conditions. Mummified seals, curious natural artifacts found scattered throughout Dry Valleys, alter their underlying soil environment by stabilizing temperatures, elevating relative humidity and reducing ultraviolet exposure. In a unique, multi-year mummified seal transplantation experiment, we found that endemic Dry Valley microbial communities responded to these changes within 3 years, resulting in a sevenfold increase in CO(2) flux and a significant reduction in biodiversity. These findings challenge prevailing ideas about Antarctic Dry Valley ecosystems and indicate that current and future environmental conditions may strongly influence the ecology of the dominant biota in the Dry Valleys.
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Affiliation(s)
- Grace Tiao
- The International Centre for Terrestrial Antarctic Research, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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50
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Lazarevic V, Whiteson K, Gaïa N, Gizard Y, Hernandez D, Farinelli L, Osterås M, François P, Schrenzel J. Analysis of the salivary microbiome using culture-independent techniques. J Clin Bioinforma 2012; 2:4. [PMID: 22300522 PMCID: PMC3296672 DOI: 10.1186/2043-9113-2-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 02/02/2012] [Indexed: 11/10/2022] Open
Abstract
Background The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated. Methods We explored the bacterial community composition in the saliva sample using metagenomic whole genome shotgun (WGS) sequencing, the extraction of 16S rRNA gene fragments from metagenomic sequences (16S-WGS) and high-throughput sequencing of PCR-amplified bacterial 16S rDNA gene (16S-HTS) regions V1 and V3. Results The hierarchical clustering of data based on the relative abundance of bacterial genera revealed that distances between 16S-HTS datasets for V1 and V3 regions were greater than those obtained for the same V region with different numbers of PCR cycles. Datasets generated by 16S-HTS and 16S-WGS were even more distant. Finally, comparison of WGS and 16S-based datasets revealed the highest dissimilarity. The analysis of the 16S-HTS, WGS and 16S-WGS datasets revealed 206, 56 and 39 bacterial genera, respectively, 124 of which have not been previously identified in salivary microbiomes. A large fraction of DNA extracted from saliva corresponded to human DNA. Based on sequence similarity search against completely sequenced genomes, bacterial and viral sequences represented 0.73% and 0.0036% of the salivary metagenome, respectively. Several sequence reads were identified as parts of the human herpesvirus 7. Conclusions Analysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland.
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