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Oberreiter V, Gelabert P, Brück F, Franz S, Zelger E, Szedlacsek S, Cheronet O, Cano FT, Exler F, Zagorc B, Karavanić I, Banda M, Gasparyan B, Straus LG, Gonzalez Morales MR, Kappelman J, Stahlschmidt M, Rattei T, Kraemer SM, Sawyer S, Pinhasi R. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. Sci Rep 2024; 14:19388. [PMID: 39169089 PMCID: PMC11339378 DOI: 10.1038/s41598-024-69741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
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Affiliation(s)
- Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Florian Brück
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Franz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Evelyn Zelger
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Sophie Szedlacsek
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | | | - Florian Exler
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Marko Banda
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, USA
- EvoAdapta Group Universidad de Cantabria, Santander, Spain
| | - Manuel R Gonzalez Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Gobierno de Cantabria, Banco Santander, Spain
| | - John Kappelman
- Department of Anthropology and Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA
| | - Mareike Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan M Kraemer
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institut für Analytische Chemie, University of Vienna, Vienna, Austria
- Forschungsverbund Umwelt und Klima, University of Vienna, Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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2
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Hong BY, Driscoll M, Gratalo D, Jarvie T, Weinstock GM. Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies. Int J Mol Sci 2024; 25:2966. [PMID: 38474213 DOI: 10.3390/ijms25052966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Next-generation sequencing technology has driven the rapid advancement of human microbiome studies by enabling community-level sequence profiling of microbiomes. Although all microbiome sequencing methods depend on recovering the DNA from a sample as a first critical step, lysis methods can be a major determinant of microbiome profile bias. Gentle enzyme-based DNA preparation methods preserve DNA quality but can bias the results by failing to open difficult-to-lyse bacteria. Mechanical methods like bead beating can also bias DNA recovery because the mechanical energy required to break tougher cell walls may shear the DNA of the more easily lysed microbes, and shearing can vary depending on the time and intensity of beating, influencing reproducibility. We introduce a non-mechanical, non-enzymatic, novel rapid microbial DNA extraction procedure suitable for 16S rRNA gene-based microbiome profiling applications that eliminates bead beating. The simultaneous application of alkaline, heat, and detergent ('Rapid' protocol) to milligram quantity samples provided consistent representation across the population of difficult and easily lysed bacteria equal to or better than existing protocols, producing sufficient high-quality DNA for full-length 16S rRNA gene PCR. The novel 'Rapid' method was evaluated using mock bacterial communities containing both difficult and easily lysed bacteria. Human fecal sample testing compared the novel Rapid method with a standard Human Microbiome Project (HMP) protocol for samples from lung cancer patients and controls. DNA recovered from both methods was analyzed using 16S rRNA gene sequencing of the V1V3 and V4 regions on the Illumina platform and the V1V9 region on the PacBio platform. Our findings indicate that the 'Rapid' protocol consistently yielded higher levels of Firmicutes species, which reflected the profile of the bacterial community structure more accurately, which was confirmed by mock community evaluation. The novel 'Rapid' DNA lysis protocol reduces population bias common to bead beating and enzymatic lysis methods, presenting opportunities for improved microbial community profiling, combined with the reduction in sample input to 10 milligrams or less, and it enables rapid transfer and simultaneous lysis of 96 samples in a standard plate format. This results in a 20-fold reduction in sample handling time and an overall 2-fold time advantage when compared to widely used commercial methods. We conclude that the novel 'Rapid' DNA extraction protocol offers a reliable alternative for preparing fecal specimens for 16S rRNA gene amplicon sequencing.
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Affiliation(s)
- Bo-Young Hong
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Massarelli C, Campanale C. Climatic, bioclimatic, and pedological influences on the vegetation classification of "Bosco dell'Incoronata" in Southern Italy. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2023. [DOI: 10.1007/s12210-023-01146-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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4
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Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment. Microorganisms 2022; 10:microorganisms10122505. [PMID: 36557758 PMCID: PMC9784657 DOI: 10.3390/microorganisms10122505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.
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Nie W, Zheng X, Wang S, Ahmad I, Zhu B. Genome Resource of Ancylobacter pratisalsi E130 T: A Novel Plant-Growth-Promoting Bacterium Isolated from the Rhizosphere. PHYTOPATHOLOGY 2022; 112:729-731. [PMID: 34353121 DOI: 10.1094/phyto-06-21-0251-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Ancylobacter pratisalsi sp. nov. strain E130T is a Gram-negative, nonmotile, aerobic, and rod-shaped bacterium that was recently isolated from the rhizosphere of Plantago winteri Wirtg. from a natural salt meadow. This strain was described as novel species in genus Ancylobacter; however, information about its complete genome has yet not been reported. In this study, its genome was completely sequenced by PacBio SMRT cell platform, analyzed, and compared with other selected complete genome sequences of Ancylobacter to elucidate its potential plant growth promotion abilities. The genomic analysis revealed that the genome of strain E130T consists of one circular DNA chromosome of 4,618,530 bp with a GC content of 66% and one plasmid of 159,741 bp with a GC content of 64.13%. The entire genome contains 4,322 predicted coding genes, 49 transfer RNAs, and 6 ribosomal RNA genes. Genome analysis identified a siderophore natural product biosynthesis cluster, which produces fuscachelin. Knockout of several key genes in this cluster significantly reduces the plant-growth-promotion ability of the strain E130T. In addition to plant-growth promotion, the strain E130T can grow well on 5% NaCl (wt/vol), indicating that this strain is a potential bioresource for successful production of economic crops in alkaline soil.
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Affiliation(s)
- Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Xin Zheng
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari, 61100, Pakistan
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai 200240, China
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6
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Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR. Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data. J Microbiol Methods 2021; 188:106271. [PMID: 34146605 DOI: 10.1016/j.mimet.2021.106271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023]
Abstract
Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.
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Affiliation(s)
- Natascha Lewe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Syrie Hermans
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura T Kelly
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Barbara Weisbrod
- Human and Environmental Toxicology, Department of Biology, Universität Konstanz, 78457 Konstanz, Germany
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Robert A Keyzers
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand.
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Sakai Y. Improvements in Extraction Methods of High-molecular-weight DNA from Soils by Modifying Cell Lysis Conditions and Reducing Adsorption of DNA onto Soil Particles. Microbes Environ 2021; 36. [PMID: 34234043 PMCID: PMC8446751 DOI: 10.1264/jsme2.me21017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-molecular-weight DNA (HMW DNA) extracted from soil is useful for examined the functions and diversity of soil organisms, the majority of which are difficult to culture. In the present study, the procedures used to extract HMW DNA from soil samples were improved. The grinding of soil samples with liquid nitrogen followed by a lysozyme treatment at 45°C for 1 h and an incubation with protease and SDS at 50°C for 5 h increased the size and yield of HMW DNA extracted from these samples. In the soil group Andosols, the addition of boiled sonicated salmon DNA was effective for HMW DNA extraction.
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Affiliation(s)
- Yoriko Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO)
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8
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Guerra V, Beule L, Lehtsaar E, Liao HL, Karlovsky P. Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer. Microorganisms 2020; 8:microorganisms8040532. [PMID: 32272709 PMCID: PMC7232467 DOI: 10.3390/microorganisms8040532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 11/23/2022] Open
Abstract
As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology.
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Affiliation(s)
- Victor Guerra
- North Florida Research and Education Center, Soil and Water Sciences Department, University of Florida, Quincy, FL 32351, USA; (V.G.); (H.-L.L.)
| | - Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
- Correspondence:
| | - Ena Lehtsaar
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
| | - Hui-Ling Liao
- North Florida Research and Education Center, Soil and Water Sciences Department, University of Florida, Quincy, FL 32351, USA; (V.G.); (H.-L.L.)
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
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Affiliation(s)
- Alex Weir
- Faculty of Environmental & Forest Biology, SUNY College of Environmental Science & Forestry, 350 Illick Hall, 1 Forestry Drive, Syracuse, New York 13210
| | - Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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Acevedo-Barrera A, García-Valenzuela A. Theoretical assessment of single-frequency electrical sensors for continuous monitoring of cell lysis in dilute suspensions. SENSING AND BIO-SENSING RESEARCH 2018. [DOI: 10.1016/j.sbsr.2018.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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11
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The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms. MICROMACHINES 2018; 9:mi9080367. [PMID: 30424300 PMCID: PMC6187716 DOI: 10.3390/mi9080367] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022]
Abstract
Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.
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12
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Pecchia S, Da Lio D. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil. J Microbiol Methods 2018; 151:118-128. [PMID: 29959955 DOI: 10.1016/j.mimet.2018.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/30/2022]
Abstract
The 'Nucleic Acid Lateral Flow Immunoassay' (NALFIA) using a generic 'Lateral Flow Device' (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will develop on the LFD strip in addition to the control band. Species-specific primers for M. phaseolina based on the rDNA intergenic spacer (IGS) were developed and their specificity was checked and confirmed using 20 isolates of M. phaseolina and other 16 non-target fungi. A DNA extraction protocol based on a bead-beating technique using silica beads, skimmed milk and PVP was also developed. The M. phaseolina specific primers MP102F/MP102R, 5' labelled with biotin and FITC respectively, were used in the PCR-NALFIA assay to identify the pathogen starting from mycelium or microsclerotia. Microsclerotia of M. phaseolina (1, 10, 100 and 200) were manipulated under a stereomicroscope and their DNA was extracted using microsclerotia alone or mixed with different types of soil. The resulting DNA, used for the PCR-NALFIA assay, provided positive results for all the samples tested. A semi-quantitative grey-scale reference card based on the PCR-NALFIA assay using intervals corresponding to microsclerotia soil number was developed. For this purpose, the normalized pixel grey volumes obtained after a densitometric analysis of the test line intensity generated by the LFD dipsticks were used.
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Affiliation(s)
- Susanna Pecchia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy.
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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13
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Okasaka M, Kubota K, Yamasaki E, Yang J, Takata S. Evaluation of anionic surfactants effects on the skin barrier function based on skin permeability. Pharm Dev Technol 2018; 24:99-104. [PMID: 29323614 DOI: 10.1080/10837450.2018.1425885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Anionic surfactants are often used for cleaning and pharmaceutical purposes because of their strong surfactancy and foaming property. However, they are rarely ingested orally, the skin is a part of the human body most affected by surfactants. Barrier function of the skin is very strong, but the anionic surfactants can cause serious damages to it. Recently, amino acid-based surfactants have attracted attention as a safer option owing to their biocompatibility. Cytotoxicity examinations revealed that the amino acid-based surfactants are superior to sulfate-based surfactants. However, a systematical and comprehensive study related to the effect of these surfactants on skin barrier function has not yet been reported. In this work, skin permeation test using the skin of hairless mice and HPLC method is carried out. The material transmission speed through skin in a steady state was different between each surfactant treatment. We performed a comprehensive analysis of the effect of surfactants on skin barrier function and defined Transmission Index as an index for the degree of effect of surfactants. Glutamate series amino acid-based surfactant were effective to Transmission Index and we guessed the cause was due to adsorption. Based on the finding this study, we suggest using adsorptive property as a measure to the effect on the skin barrier function.
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Affiliation(s)
- Mana Okasaka
- a Department of Fashion and Beauty Sciences , Osaka Shoin Women's University , Higashiosaka-shi , Osaka , Japan.,b Division in Beauty and Fashion Studies, Graduate School of Human Sciences , Osaka Shoin Women's University , Higashiosaka-shi , Osaka , Japan
| | - Koji Kubota
- c Department of Pharmacy , Iwaki Meisei University , Iwaki-shi , Fukushima , Japan.,d Department of Pharmacy , Yasuda Women's University , Hiroshima-shi , Hiroshima , Japan
| | - Emi Yamasaki
- e Beauty Hi-tech Innovation Co., Ltd , Kobe-shi , Hyogo , Japan
| | - Jianzhong Yang
- e Beauty Hi-tech Innovation Co., Ltd , Kobe-shi , Hyogo , Japan.,f Asian Scalp Health Research Center , Kobe-shi , Hyogo , Japan
| | - Sadaki Takata
- a Department of Fashion and Beauty Sciences , Osaka Shoin Women's University , Higashiosaka-shi , Osaka , Japan.,b Division in Beauty and Fashion Studies, Graduate School of Human Sciences , Osaka Shoin Women's University , Higashiosaka-shi , Osaka , Japan
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14
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RedCorn R, Engelberth AS. Opportunities to improve the conversion of food waste to lactate: Fine-tuning secondary factors. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2017; 35:1112-1120. [PMID: 28825368 DOI: 10.1177/0734242x17723978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Extensive research has demonstrated the potential for bioconversion of food waste to lactate, with major emphasis on adjusting temperature, pH, and loading rate of the fermentation. Each of these factors has a significant effect on lactate production; however, additional secondary factors have received little attention. Here we investigate three additional factors where opportunities exist for process improvement: freezing of samples during storage, discontinuous pH control, and holdover of fermentation broth between fermentations. Freezing samples prior to fermentation was shown to reduce the production rate of lactate by 8%, indicating freeze-thaw should be avoided in experiments. Prior work indicated a trade-off in pH control strategies, where discontinuous pH control correlated with higher lactate accumulation while continuous pH control correlated with higher production rate. Here we demonstrate that continuous pH control can achieve both higher lactate accumulation and higher production rate. Finally, holding over fermentation broth was shown to be a simple method to improve production rate (by 18%) at high food waste loading rates (>140 g volatile solids L-1) but resulted in lower lactate accumulation (by 17%). The results inform continued process improvements within the waste treatment of food waste through fermentation to lactic acid.
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Affiliation(s)
- Raymond RedCorn
- 1 Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, USA
- 2 Ecological Sciences and Engineering Interdisciplinary Graduate Program, Purdue University, USA
| | - Abigail S Engelberth
- 1 Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, USA
- 3 Environmental and Ecological Engineering, Purdue University, USA
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Suarez C, Ratering S, Schäfer J, Schnell S. Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg. Int J Syst Evol Microbiol 2017; 67:4500-4506. [PMID: 28945527 DOI: 10.1099/ijsem.0.002320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130T to A. rudongensis DSM 17131T, A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Johanna Schäfer
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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Meier A, Singh MK, Kastner A, Merten D, Büchel G, Kothe E. Microbial communities in carbonate rocks-from soil via groundwater to rocks. J Basic Microbiol 2017; 57:752-761. [PMID: 28681946 DOI: 10.1002/jobm.201600643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 11/10/2022]
Abstract
Microbial communities in soil, groundwater, and rock of two sites in limestone were investigated to determine community parameters differentiating habitats in two lithostratigraphic untis. Lower Muschelkalk and Middle Muschelkalk associated soils, groundwater, and rock samples showed different, but overlapping microbial communities linked to carbon fluxes. The microbial diversities in soil were highest, groundwater revealed overlapping taxa but lower diversity, and rock samples were predominantly characterized by endospore forming bacteria and few archaea. Physiological profiles could establish a differentiation between habitats (soil, groundwater, rock). From community analyses and physiological profiles, different element cycles in limestone could be identified for the three habitats. While in soil, nitrogen cycling was identified as specific determinant, in rock methanogenesis linked carbonate rock to atmospheric methane cycles. These patterns specifically allowed for delineation of lithostratigraphic connections to physiological parameters.
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Affiliation(s)
- Aileen Meier
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Manu K Singh
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Anne Kastner
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dirk Merten
- Institute of Geosciences, Applied Geology, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Büchel
- Institute of Geosciences, Applied Geology, Friedrich Schiller University Jena, Jena, Germany
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
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Comparison of two bacterial DNA extraction methods from non-polluted and polluted soils. Folia Microbiol (Praha) 2017; 63:85-92. [PMID: 28667598 DOI: 10.1007/s12223-017-0530-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
DNA extraction from soil samples is a critical step for molecular biology analyses. The present study compared the efficiency of two DNA isolation methods from non-polluted and polluted soils with or without the presence of a plant. Both applied methods used chemical and physical lyses, but method 1 had an additional physical disruption. The main difference between these two methods was the humic acid purification technique as it was carried out during cell lysis for method 1 and after cell lysis for method 2. Samples were assessed on the basis of their yield and DNA purity as well as their bacterial quantity and diversity. Based on our results, method 1 proved to be more effective at removing protein and RNA, whereas method 2 proved to be more effective at removing humic acids. Although no differences were obtained in terms of the DNA yield, both the bacterial quantity and community structure were affected by the method used. Method 1 allowed for the recovery of more information than method 2, and polluted soil was more sensitive to the DNA extraction procedure. We recommend carefully selecting the DNA extraction method, especially when soil is disturbed.
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Rapid and efficient method to extract metagenomic DNA from estuarine sediments. 3 Biotech 2017; 7:182. [PMID: 28664369 DOI: 10.1007/s13205-017-0846-y] [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: 04/20/2017] [Accepted: 05/24/2017] [Indexed: 10/19/2022] Open
Abstract
Metagenomic DNA from sediments of selective estuaries of Goa, India was extracted using a simple, fast, efficient and environment friendly method. The recovery of pure metagenomic DNA from our method was significantly high as compared to other well-known methods since the concentration of recovered metagenomic DNA ranged from 1185.1 to 4579.7 µg/g of sediment. The purity of metagenomic DNA was also considerably high as the ratio of absorbance at 260 and 280 nm ranged from 1.88 to 1.94. Therefore, the recovered metagenomic DNA was directly used to perform various molecular biology experiments viz. restriction digestion, PCR amplification, cloning and metagenomic library construction. This clearly proved that our protocol for metagenomic DNA extraction using silica gel efficiently removed the contaminants and prevented shearing of the metagenomic DNA. Thus, this modified method can be used to recover pure metagenomic DNA from various estuarine sediments in a rapid, efficient and eco-friendly manner.
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20
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Seasonal and Interannual Fluctuation of the Microbial Soil Community in a Maize Field under Long-Term Conservation Agriculture Management. SUSTAINABILITY 2017. [DOI: 10.3390/su9050778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Wang X, Cho KS, Son A. Ultrasonication as a rapid and high yield DNA extraction method for bacterial gene quantification by NanoGene assay. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0465-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
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24
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Beyer A, Rzanny M, Weist A, Möller S, Burow K, Gutmann F, Neumann S, Lindner J, Müsse S, Brangsch H, Stoiber-Lipp J, Lonschinski M, Merten D, Büchel G, Kothe E. Aquifer community structure in dependence of lithostratigraphy in groundwater reservoirs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:19342-19351. [PMID: 26002361 DOI: 10.1007/s11356-015-4682-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/08/2015] [Indexed: 06/04/2023]
Abstract
Groundwater microbiology with respect to different host rocks offers new possibilities to describe and map the habitat harboring approximately half of Earths' biomass. The Thuringian Basin (Germany) contains formations of the Permian (Zechstein) and Triassic (Muschelkalk and Buntsandstein) with outcrops and deeper regions at the border and central part. Hydro(geo)chemistry and bacterial community structure of 11 natural springs and 20 groundwater wells were analyzed to define typical patterns for each formation. Widespread were Gammaproteobacteria, while Bacilli were present in all wells. Halotolerant and halophilic taxa were present in Zechstein. The occurrence of specific taxa allowed a clear separation of communities from all three lithostratigraphic groups. These specific taxa could be used to follow fluid movement, e.g., from the underlying Zechstein or from nearby saline reservoirs into Buntsandstein aquifers. Thus, we developed a new tool to identify the lithostratigraphic origin of sources in mixed waters. This was verified with entry of surface water, as species not present in the underground Zechstein environments were isolated from the water samples. Thus, our tool shows a higher resolution as compared to hydrochemistry, which is prone to undergo fast dilution if water mixes with other aquifers. Furthermore, the bacteria well adapted to their respective environment showed geographic clustering allowing to differentiate regional aquifers.
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Affiliation(s)
- Andrea Beyer
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Michael Rzanny
- Institute of Ecology, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Aileen Weist
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Silke Möller
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Katja Burow
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Falko Gutmann
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Stefan Neumann
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Julia Lindner
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Steffen Müsse
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Hanka Brangsch
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Jennifer Stoiber-Lipp
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Martin Lonschinski
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Dirk Merten
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Georg Büchel
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Erika Kothe
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany.
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Kathiravan MN, Gim GH, Ryu J, Kim PI, Lee CW, Kim SW. Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil. J Microbiol 2015; 53:767-75. [DOI: 10.1007/s12275-015-5454-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/02/2015] [Accepted: 10/02/2015] [Indexed: 11/29/2022]
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Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples. Folia Microbiol (Praha) 2015; 60:551-8. [DOI: 10.1007/s12223-015-0403-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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Lever MA, Torti A, Eickenbusch P, Michaud AB, Šantl-Temkiv T, Jørgensen BB. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Front Microbiol 2015; 6:476. [PMID: 26042110 PMCID: PMC4436928 DOI: 10.3389/fmicb.2015.00476] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/30/2015] [Indexed: 11/19/2022] Open
Abstract
A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.
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Affiliation(s)
- Mark A Lever
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Andrea Torti
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | | | - Alexander B Michaud
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Tina Šantl-Temkiv
- Microbiology Section, Department of Bioscience, Aarhus University Aarhus, Denmark ; Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University Aarhus, Denmark
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
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Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). J Microbiol Methods 2015; 112:104-17. [DOI: 10.1016/j.mimet.2015.03.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 01/08/2023]
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He X, Zhang Q, Cooney MJ, Yan T. Biodegradation of fat, oil and grease (FOG) deposits under various redox conditions relevant to sewer environment. Appl Microbiol Biotechnol 2015; 99:6059-68. [PMID: 25715780 DOI: 10.1007/s00253-015-6457-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/30/2015] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
Abstract
Fat, oil and, grease (FOG) deposits are one primary cause of sanitary sewer overflows (SSOs). While numerous studies have examined the formation of FOG deposits in sewer pipes, little is known about their biodegradation under sewer environments. In this study, FOG deposit biodegradation potential was determined by studying the biodegradation of calcium palmitate in laboratory under aerobic, nitrate-reducing, sulfate-reducing, and methanogenic conditions. Over 110 days of observation, calcium palmitate was biodegraded to CO2 under aerobic and nitrate-reducing conditions. An approximate 13 times higher CO2 production rate was observed under aerobic condition than under nitrate-reducing condition. Under sulfate-reducing condition, calcium palmitate was recalcitrant to biodegradation as evidenced by small reduction in sulfate. No evidence was found to support calcium palmitate degradation under methanogenic condition in the simulated sewer environment. Dominant microbial populations in the aerobic and nitrate-reducing microcosms were identified by Illumina seqeuncing, which may contain the capability to degrade calcium palmitate under both aerobic and nitrate-reducing conditions. Further study on these populations and their functional genes could shed more light on this microbial process and eventually help develop engineering solutions for SSOs control in the future.
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Affiliation(s)
- Xia He
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
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Irwin P, Nguyen L, He Y, Paoli G, Gehring A, Chen CY. The near-quantitative sampling of genomic DNA from various food-borne Eubacteria. BMC Microbiol 2014; 14:326. [PMID: 25551371 PMCID: PMC4302497 DOI: 10.1186/s12866-014-0326-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The disruption of the bacterial cell wall plays an important part in achieving quantitative extraction of DNA from Eubacteria essential for accurate analyses of genetic material recovered from environmental samples. RESULTS In this work we have tested a dozen commercial bacterial genomic DNA extraction methodologies on an average of 7.70 × 10(6) (±9.05%), 4.77 × 10(8) (±31.0%), and 5.93 × 10(8) (±4.69%) colony forming units (CFU) associated with 3 cultures (n = 3) each of Brochothrix thermosphacta (Bt; Gram-positive), Shigella sonnei (Ss; Gram-negative), and Escherichia coli O79 (Ec; Gram-negative). We have utilized real-time PCR (qPCR) quantification with two specific sets of primers associated with the 16S rRNA "gene" to determine the number of copies CFU(-1) by comparing the unknown target DNA qPCR results with standards for each primer set. Based upon statistical analyses of our results, we determined that the Agencourt Genfind v2, High Pure PCR Template Prep Kit, and Omnilyse methods consistently provided the best yield of genomic DNA ranging from 141 to 934, 8 to 21, and 16 to 27 16S rDNA copies CFU(-1) for Bt, Ss, and Ec. If one assumes 6-7 copies of the 16S rRNA gene per genome, between 1 and 3 genomes per actively dividing cell and ≥ 100 cells CFU(-1) for Bt (found to be a reasonable assumption using an optical method expounded upon herein) or between 1 and 2 cells CFU(-1) for either Ss or Ec, then the Omnilyse procedure provided nearly quantitative extraction of genomic DNA from these isolates (934 ± 19.9 copies CFU(-1) for Bt; 20.8 ± 2.68 copies CFU(-1) for Ss; 26.9 ± 3.39 copies CFU(-1) for Ec). The Agencourt, High Pure, and Omnilyse technologies were subsequently assessed using 5 additional Gram-positive and 10 Gram-negative foodborne isolates (n = 3) using a set of "universal" 16S rDNA primers. CONCLUSION Overall, the most notable DNA extraction method was found to be the Omnilyse procedure which is a "bead blender" technology involving high frequency agitation in the presence of zirconium silicate beads.
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Affiliation(s)
- Peter Irwin
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Ly Nguyen
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Yiping He
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - George Paoli
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Andrew Gehring
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Chin-Yi Chen
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
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Shi YW, Zhang X, Lou K. Analysis of endophytic bacterial community composition by 16S rDNA clone library in Achnatherum inebrians. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Sharma S, Vakhlu J. Metagenomics as advanced screening methods for novel microbial metabolites. Microb Biotechnol 2014. [DOI: 10.1201/b17587-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Abstract
Microbes in nature are rarely amenable to growth by standard microbiological methods, with the majority being unculturable. Metagenomic methods help to bypass and overcome the limitations of traditional culturing method; wherein total community DNA is isolated, cloned into suitable vector and host systems. However, isolation of total community DNA itself remains a challenge. In this study five methods of total community DNA isolation from three different mangrove soils were evaluated to test its PCR amenability. The yield and purity of the isolated DNA was also analysed. The quantity of DNA by all 5 methods although reasonably high, contained residual humic contaminants. Of the five, the method employing liquid nitrogen yielded readily amplifiable DNA, while that by all others required further downstream processing to achieve purity and PCR amenability.
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Wang X, Lee BT, Son A. Physical lysis only (PLO) methods suitable as rapid sample pretreatment for qPCR assay. Appl Microbiol Biotechnol 2014; 98:8719-28. [PMID: 25219535 DOI: 10.1007/s00253-014-6064-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/29/2014] [Accepted: 08/30/2014] [Indexed: 12/30/2022]
Abstract
Quantitative PCR (qPCR) enables rapid and sensitive gene quantification and is widely used in genomics, such as biological, medical, environmental, and food sciences. However, sample pretreatment requires the use of conventional DNA extraction kits which are time-consuming and labor intensive. In this study, we investigated four physical lysis only (PLO) methods which are rapid and could serve as alternatives to conventional DNA extraction kits. These PLO methods are bead mill, heating, sonication, and freeze-thaw. Using ethidium bromide-based assay, their performance was evaluated and compared. The effects of cell debris and its removal were also investigated. Bead mill method without cell debris removal appeared to yield the best qPCR results among the four PLO methods. In addition, bead mill method also performed better than conventional DNA extraction kits. It is probably due to the substantial loss of DNA material during the extensive purification of the conventional DNA extraction kits. The bead mill method has been demonstrated to successfully quantify 10(2) to 10(7) copies of the PAH-RHDα gene of Pseudomonas putida.
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Affiliation(s)
- Xiaofang Wang
- Department of Civil Engineering, Auburn University, Auburn, AL, 36849, USA
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An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region. Mol Biol Int 2014; 2014:518960. [PMID: 25302120 PMCID: PMC4181777 DOI: 10.1155/2014/518960] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/10/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
The need for identification of soil microbial community mainly depends on direct extraction of DNA from soil, a multifaceted environment that is a major pool for microbial genetic diversity. The soil DNA extraction procedures usually suffer from two major problems, namely, inappropriate rupturing of cells and contamination with humic substances. In the present study, five protocols for single type of rhizospheric soil were investigated and their comparison indicated that the inclusion of 120 mM phosphate buffered saline (PBS) for washing and mannitol in the lysis buffer allowed the processing of soil sample in minimal time with no specific equipment requirement. Furthermore, DNA purity and yield were also improved, which allowed the exploitation of genetic potential of soil microbes within soil sample thereby facilitating the amplification of metagenomic DNA. The effectiveness of methods was analyzed using random amplification of polymorphic DNA. The banding patterns revealed that both the abundance and the composition of indigenous microbial community depend on the DNA recovery method.
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Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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38
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Isolation of PCR quality microbial community DNA from heavily contaminated environments. J Microbiol Methods 2014; 102:1-7. [DOI: 10.1016/j.mimet.2014.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 04/11/2014] [Accepted: 04/11/2014] [Indexed: 11/24/2022]
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Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum. Int J Syst Evol Microbiol 2014; 64:1202-1209. [DOI: 10.1099/ijs.0.061200-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two motile, Gram-staining-negative, aerobic, rod-shaped bacteria designated strains E48T and E49T were isolated from the rhizosphere of Hordeum secalinum from a natural salt meadow near Münzenberg, Germany. 16S rRNA gene sequence similarity analysis revealed that strains E48T and E49T shared similarities of 97.6 % with
Rheinheimera pacifica
KMM 1406T and 98.5 % with
Rheinheimera nanhaiensis
E407-8T, respectively. Major fatty acids of strain E48T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 1ω8c, and of strain E49T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The DNA G+C contents were 50.5 mol% (E48T) and 50.0 mol% (E49T). Strains E48T and E49T grew at 4–37 °C (optimum 28 °C) and with 0–6 % NaCl (optimum 0–3 %) and 0–5 % NaCl (optimum 0–3 %), respectively. The potential for nitrogen fixation by strains E48T and E49T was evaluated by molecular techniques and the acetylene reduction assay. The DNA–DNA hybridization, physiological and molecular data demonstrated that strains E48T and E49T represent two novel species of the genus
Rheinheimera
, and therefore the names Rheinheimera hassiensis sp. nov. (type strain E48T = LMG 27268T = KACC 17070T) and Rheinheimera muenzenbergensis sp. nov. (type strain E49T = LMG 27269T = KACC 17071T) are proposed.
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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Sharma S, Sharma KK, Kuhad RC. An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments. J Appl Microbiol 2014; 116:923-33. [PMID: 24329912 DOI: 10.1111/jam.12420] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/05/2013] [Accepted: 12/09/2013] [Indexed: 11/30/2022]
Abstract
AIMS An attempt was made to optimize a new protocol for isolation of pure metagenomic DNA from soil samples. METHODS AND RESULTS Various chemicals (FeCl3 , MgCl2 , CaCl2 and activated charcoal) were tested for their efficacy in isolation of metagenomic DNA from different soil and compost samples. Among these trials, charcoal and MgCl2 when used in combination yielded highly pure DNA free from humic acids and other contaminants. The DNA extracted with the optimized protocol was readily digested, amplified and cloned. Moreover, compared with a well-established commercial DNA isolation kit (UltraClean™ Soil DNA Isolation Kit), our method for DNA isolation was found to be economical. This demonstrated that the method developed can be applied to a wide variety of soil samples and allows handling of multiple samples at a given time. CONCLUSIONS The optimized protocol developed has successfully yielded pure metagenomic DNA amenable to biotechnological manipulations. SIGNIFICANCE AND IMPACT OF THE STUDY A user-friendly and economical protocol for isolation of DNA from soil and compost samples has been developed.
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Affiliation(s)
- S Sharma
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi, India
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41
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Abramov SM, Sadraddinova ER, Shestakov AI, Voronin OG, Karyakin AA, Zorin NA, Netrusov AI. Turning cellulose waste into electricity: hydrogen conversion by a hydrogenase electrode. PLoS One 2013; 8:e83004. [PMID: 24312437 PMCID: PMC3842985 DOI: 10.1371/journal.pone.0083004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L(-1) h(-1) and 1 mM L(-1) h(-1), respectively. An enzymatic fuel cell (EFC) with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h) to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value.
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Affiliation(s)
- Sergey M. Abramov
- Biological Faculty of M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
| | | | - Andrey I. Shestakov
- Biological Faculty of M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Oleg G. Voronin
- Chemical Faculty of M.V. Lomonosov Moscow State University, Moscow, Russia
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Wunderlin T, Junier T, Roussel-Delif L, Jeanneret N, Junier P. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:911-924. [PMID: 24249300 DOI: 10.1111/1758-2229.12094] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
In this study, we developed and validated a culture-independent method for diversity surveys to specifically detect endospore-forming Firmicutes. The global transcription regulator of sporulation (spo0A) was identified as a gene marker for endospore-forming Firmicutes. To enable phylogenetic classification, we designed a set of primers amplifying a 602 bp fragment of spo0A that we evaluated in pure cultures and environmental samples. The amplification was positive for 35 strains from 11 genera, yet negative for strains from Alicyclobacillus and Sulfobacillus. We also evaluated various DNA extraction methods because endospores often result in reduced yields. Our results demonstrate that procedures utilizing increased physical force improve DNA extraction. An optimized DNA extraction method on biomass pre-extracted from the environmental sample source (indirect DNA extraction) followed by amplification with the aforementioned primers for spo0A was then tested in sediments from two different sources. Specifically, we validated our culture-independent diversity survey methodology on a set of 8338 environmental spo0A sequences obtained from the sediments of Lakes Geneva (Switzerland) and Baikal (Russia). The phylogenetic affiliation of the environmental sequences revealed a substantial number of new clades within endospore-formers. This novel culture-independent approach provides a significant experimental improvement that enables exploration of the diversity of endospore-forming Firmicutes.
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Affiliation(s)
- Tina Wunderlin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2000, Switzerland
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43
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Suarez C, Ratering S, Kramer I, Schnell S. Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio. Int J Syst Evol Microbiol 2013; 64:481-486. [PMID: 24105943 DOI: 10.1099/ijs.0.054817-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-reaction-negative, aerobic, nitrogen-fixing, rod-shaped bacteria, designated strains E20 and E50(T), were isolated from the rhizosphere of salt meadow plants Plantago winteri and Hordeum secalinum, respectively, near Münzenberg, Germany. Based on the 16S rRNA gene sequence analysis both strains E20 and E50(T) are affiliated with the genus Cellvibrio, sharing the highest similarity with Cellvibrio gandavensis LMG 18551(T) (96.4%) and (97.1%), respectively. Strains E20 and E50(T) were oxidase and catalase-positive, grew at a temperature range between 16 and 37 °C and in the presence of 0-5% NaCl (w/v). The DNA G+C contents were 52.1 mol% (E20) and 51.6 mol% (E50(T)). Major fatty acids of strains E20 and E50(T) were summed feature 3 (C16 : 1ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c, C(12 : 0), C(18 : 0) and C(12 : 0) 3-OH. The DNA-DNA relatedness of the strains to Cellvibrio gandavensis LMG 18551(T) was 39% for strain E20 and 58% for strain E50(T). The nitrogen fixation capability of strains E20 and E50(T) was confirmed by the acetylene reduction assay. On the basis of our polyphasic taxonomic study, strains E20 and E50(T) represent a novel species of the genus Cellvibrio, for which the name Cellvibrio diazotrophicus is proposed. The type strain of Cellvibrio diazotrophicus is E50(T) ( = LMG 27267(T) = KACC 17069(T)). An emended description of the genus Cellvibrio is proposed based on the capability of fixing nitrogen and growth in presence of up to 5% NaCl (w/v).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Irina Kramer
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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44
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Gentry-Shields J, Wang A, Cory RM, Stewart JR. Determination of specific types and relative levels of QPCR inhibitors in environmental water samples using excitation-emission matrix spectroscopy and PARAFAC. WATER RESEARCH 2013; 47:3467-3476. [PMID: 23601829 DOI: 10.1016/j.watres.2013.03.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 06/02/2023]
Abstract
Assays that utilize PCR offer powerful tools to detect pathogens and other microorganisms in environmental samples. However, PCR inhibitors present in nucleic acid extractions can increase a sample's limit of detection, skew calculated marker concentrations, or cause false-negative results. It would be advantageous to predict which samples contain various types and levels of PCR inhibitors, especially the humic and fulvic acids that are frequently cited as PCR inhibitors in natural water samples. This study investigated the relationships between quantitative PCR (qPCR) inhibition and the humic and fulvic content of dissolved organic matter (DOM), as well as several other measures of DOM quantity and quality, in water samples. QPCR inhibition was also compared to water quality parameters, precipitation levels, and land use adjacent to the sampling location. Results indicate that qPCR inhibition in the tested water samples was correlated to several humic substance-like, DOM components, most notably terrestrially-derived, humic-like DOM and microbially-derived, fulvic-like DOM. No correlation was found between qPCR inhibition and water quality parameters or land use, but a relationship was noted between inhibition and antecedent rainfall. This study suggests that certain fractions of humic substances are responsible for PCR inhibition from temperate, freshwater systems. PARAFAC modeling of excitation-emission matrix spectroscopy provides insight on the components of the DOM pool that impact qPCR success and may be useful in evaluating methods to remove PCR inhibitors present in samples.
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Affiliation(s)
- Jennifer Gentry-Shields
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA.
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45
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Karanis P, Aldeyarbi HM, Mirhashemi ME, Khalil KM. The impact of the waterborne transmission of Toxoplasma gondii and analysis efforts for water detection: an overview and update. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:86-99. [PMID: 22990578 DOI: 10.1007/s11356-012-1177-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 08/30/2012] [Indexed: 06/01/2023]
Abstract
The ubiquitous protozoa Toxoplasma gondii is now the subject of renewed interest, due to the spread of oocysts via water causing waterborne outbreaks of toxoplasmosis in different parts of the world. This overview discusses the different methods for detection of Toxoplasma in drinking and environmental water. It includes a combination of conventional and molecular tools for effective oocyst recovery and detection in water sources as well as factors hindering the detection of this parasite and shedding light on a promising new molecular assay for the diagnosis of Toxoplasma in environmental samples. Hopefully, this attempt will facilitate future approaches for better recovery, concentration, and detection of Toxoplasma oocysts in environmental waters.
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Affiliation(s)
- Panagiotis Karanis
- Medical and Molecular Parasitology, University Clinics of Cologne, Center of Anatomy, Institute II, Joseph-Stelzmann-Str 9, 50937 Cologne, Germany.
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46
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An optimized DNA extraction and purification method from dairy manure compost for genetic diversity analysis. World J Microbiol Biotechnol 2012; 29:815-23. [PMID: 23239373 DOI: 10.1007/s11274-012-1236-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
Abstract
An unbiased DNA extraction protocol is necessary for analysis of genetic diversity, particularly, of genes in complex environmental samples by nucleic acid techniques. In the present study, three manual extraction methods and two commonly used commercial kits, which were accompanied by two DNA purification strategies, were compared based on cell lysis efficiency, DNA and humic acid yields, PCR amplification and denaturing gradient gel electrophoresis (DGGE) analysis. The results show that in spite of higher cell lysis efficiencies of the two commercial kits, the purified DNA yields were only one-third of that obtained by the two manual methods of FTSP (Freeze-thaw-SDS-Protein K) and FTSPP (Freeze-thaw-SDS-Protein K-Polyvinylpolypyrrolidone). The purified DNA from all five methods was pure enough for successful PCR and real-time PCR amplifications in the presence of 1 μg μL(-1) BSA. However, the FTSPP extraction method with DNA purification by a Wizard(®) kit yielded the largest number of 16S rRNA gene copies and ribotypes or bands in DGGE profiles, which indicated a superiority over the other four methods. The development of this optimized DNA extraction and purification method may provide a valuable tool for further molecular analysis of compost.
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47
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Abstract
Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitations that may bias conclusions. In order to mitigate these biases, an understanding of potential biases within each stage of the experimental process is necessary. This review focuses on the biases associated with sample collection, nucleic acid extraction, processing, sequencing analyses, and Chip technologies used in microbial ecology studies.
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Affiliation(s)
- Terry C Hazen
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States.
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48
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Mishra RK, Pandey BK, Muthukumar M, Pathak N, Zeeshan M. Detection of Fusarium wilt pathogens of Psidium guajava L. in soil using culture independent PCR (ciPCR). Saudi J Biol Sci 2012; 20:51-6. [PMID: 23961219 DOI: 10.1016/j.sjbs.2012.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
Traditional culturing methods take a long time for identification of pathogenic isolates. A protocol has been developed for the detection of Fusarium from soil samples in the early stage of infection. Seventeen soil samples from different locations were collected before the onset of rains to find out the presence of Fusarium spp. population present in the soil of guava orchards and to correlate its presence with incidence of wilt. A PCR based method was developed for the molecular characterization of Fusarium using Fusarium spp. specific primer. DNA extracted by this method was free from protein and other contaminations and the yield was sufficient for PCR amplification. The primer developed in this study was amplifying ∼230 bp in all infected samples while not in healthy soil. The specificity and sensitivity of primer were tested on several Fusarium spp. and found that this primer was amplifying 10(-6) dilution of the fungal DNA. The present study facilitates the rapid detection of Fusarium spp. from infected soil samples of guava collected from different agroclimatic regions in India. A rapid detection method for pathogens and a diagnostic assay for disease would facilitate an early detection of pathogen and lead to more effective control strategies.
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Affiliation(s)
- Rupesh K Mishra
- Molecular Plant Pathology Laboratory, Division of Crop Protection, Central Institute for Subtropical Horticulture, Lucknow 227 107, India ; Department of Biotechnology, Integral University, Lucknow 226 026, India
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49
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Zhang J, Zhang Y, Quan X. Electricity assisted anaerobic treatment of salinity wastewater and its effects on microbial communities. WATER RESEARCH 2012; 46:3535-43. [PMID: 22516174 DOI: 10.1016/j.watres.2012.03.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/18/2012] [Accepted: 03/26/2012] [Indexed: 05/15/2023]
Abstract
High salinity wastewater is often difficult to treat using common anaerobic technologies. Considering that high conductivity of salinity wastewater may enhance electrodes reaction to accelerate the decomposition of volatile fatty acids produced in anaerobic digestion, a pair of electrodes was packed into an anaerobic reactor (R1) with the aim to enhance the treatment of salinity wastewater. With increasing the salt concentration (NaCl) gradually from 0 to 50 g/L in 137 days' operation, COD removal in this reactor under the voltage for the electrodes of 1.2 V was well maintained at 93%, while the COD removal in a reference anaerobic reactor without electrodes (R2) decreased to 53%. When the voltage for R1 was cut off, about 10% COD removal was declined, which was still 30 percentage points higher than that in R2. The electrodes enhanced the biodegradation of volatile fatty acids, especially propionate. Fluorescence in situ hybridization analysis confirmed that the relative abundance of propionate-utilizing bacteria in R1 was significantly higher than that in R2. PCR-DGGE analysis of bacteria and archaea domains indicated that the electric field stimulation effectively enriched salt-adapted microorganisms during the treatment.
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Affiliation(s)
- Jingxin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, No. 794, Huanghe Road, Dalian 116024, China
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50
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Lu A, Li Y, Jin S, Wang X, Wu XL, Zeng C, Li Y, Ding H, Hao R, Lv M, Wang C, Tang Y, Dong H. Growth of non-phototrophic microorganisms using solar energy through mineral photocatalysis. Nat Commun 2012; 3:768. [DOI: 10.1038/ncomms1768] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 03/01/2012] [Indexed: 11/09/2022] Open
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