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Govednik A, Eler K, Mihelič R, Suhadolc M. Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172054. [PMID: 38569950 DOI: 10.1016/j.scitotenv.2024.172054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.
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Affiliation(s)
- Anton Govednik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Klemen Eler
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Rok Mihelič
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Marjetka Suhadolc
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
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Huang K, Zhang J, Li J, Qiu H, Wei L, Yang Y, Wang C. Exploring the Impact of Primer-Template Mismatches on PCR Performance of DNA Polymerases Varying in Proofreading Activity. Genes (Basel) 2024; 15:215. [PMID: 38397205 PMCID: PMC10888005 DOI: 10.3390/genes15020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Polymerase chain reaction (PCR) is a widely used technique in gene expression analysis, diagnostics, and various molecular biology applications. However, the accuracy and sensitivity of PCR can be compromised by primer-template mismatches, potentially leading to erroneous results. In this study, we strategically designed 111 primer-template combinations with varying numbers, types, and locations of mismatches to meticulously assess their impact on qPCR performance while two distinctly different types of DNA polymerases were used. Notably, when a single-nucleotide mismatch occurred at the 3' end of the primer, we observed significant decreases in the analytical sensitivity (0-4%) with Invitrogen™ Platinum™ Taq DNA Polymerase High Fidelity, while the analytical sensitivity remained unchanged with Takara Ex Taq Hot Start Version DNA Polymerase. Leveraging these findings, we designed a highly specific PCR to amplify Babesia while effectively avoiding the genetically close Theileria. Through elucidating the critical interplay between types of DNA polymerases and primer-template mismatches, this research provides valuable insights for improving PCR accuracy and performance. These findings have important implications for researchers aiming to achieve robust qPCR results in various molecular biology applications.
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Affiliation(s)
- Ke Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
- Center of Animal Disease Control and Prevention, Songjiang District, Shanghai 201600, China
| | - Jilei Zhang
- College of Medicine, University of Illinois Chicago, Chicago, IL 60607, USA;
| | - Jing Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Haixiang Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Lanjing Wei
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA;
| | - Yi Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
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Barnewall RJ, Marsh IB, Williams TM, Cusack PMV, Sales N, Galea F, Szentirmay AN, Quinn JC. Efficiency-corrected PCR quantification for identification of prevalence and load of respiratory disease-causing agents in feedlot cattle. Aust Vet J 2022; 100:539-549. [PMID: 36328540 PMCID: PMC9804408 DOI: 10.1111/avj.13200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 01/05/2023]
Abstract
Bovine respiratory disease (BRD) is the most prevalent disease in feedlot cattle worldwide with Bovine alphaherpesvirus 1 (BoAHV1), Histophilus somni, Mannheimia haemolytica, Mycoplasma bovis, Pasteurella multocida and Trueperella pyogenes accepted to be common etiological agents associated with BRD. Although these agents are common in the upper and lower airways in clinical BRD cases, some also exist as normal flora suggesting their presence in the upper airways alone is not necessarily informative with respect to disease status or risk. To determine the relationship between presence, load and disease status, we investigated the relationship between load in the upper airways at induction and active BRD cases in feedlot cattle using efficiency-corrected PCR quantification. By this approach, we were able to accurately determine the prevalence and load of the key BRD agents in the upper respiratory tract showing that cattle in the hospital pen had a higher prevalence, and load, of these agents both singly and in combination compared to cattle sampled at feedlot induction. A combination of agents was the most accurate indicator of BRD risk with cattle with four or more agents detected in the upper airway more likely to be undergoing treatment for BRD than non-BRD ailments. In addition, M. bovis was rarely detected at feedlot induction but was identified at high prevalence in cattle in the hospital pen. These findings present a potential new technological approach for the investigation, analysis and identification of BRD-associated viral and bacterial agents for Australian feedlot systems as well as for BRD disease management and treatment.
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Affiliation(s)
- RJ Barnewall
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt UniversityLocked Bag 588Wagga WaggaNew South Wales2678Australia,Gulbali Institute for Agriculture, Water and the EnvironmentWagga WaggaNew South Wales2678Australia
| | - IB Marsh
- NSW DPI, Elizabeth Macarthur Agricultural InstitutePMB 4008NarellanNew South Wales2567Australia
| | - TM Williams
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt UniversityLocked Bag 588Wagga WaggaNew South Wales2678Australia,Gulbali Institute for Agriculture, Water and the EnvironmentWagga WaggaNew South Wales2678Australia,Present address:
School of Health, Medical and Applied Sciences, Central Queensland University554‐700 Yaamba Road, Norman GardensRockhamptonQueensland4701Australia
| | - PMV Cusack
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt UniversityLocked Bag 588Wagga WaggaNew South Wales2678Australia,Australian Livestock Production ServicesCowraNew South Wales2794Australia
| | - N Sales
- NSW DPI, Elizabeth Macarthur Agricultural InstitutePMB 4008NarellanNew South Wales2567Australia
| | - F Galea
- NSW DPI, Elizabeth Macarthur Agricultural InstitutePMB 4008NarellanNew South Wales2567Australia
| | - AN Szentirmay
- Gene Target Solutions Pty Ltd, Unit 3CBuilding 4, 256B New Line RoadDuralNew South Wales2158Australia
| | - JC Quinn
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt UniversityLocked Bag 588Wagga WaggaNew South Wales2678Australia,Gulbali Institute for Agriculture, Water and the EnvironmentWagga WaggaNew South Wales2678Australia
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Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology. FERMENTATION 2022. [DOI: 10.3390/fermentation8080365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.
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Detection by real-time PCR and conventional culture of Salmonella Typhimurium and Listeria monocytogenes adhered to stainless steel surfaces under dry conditions. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Aguilar L, Gallegos Á, Martín Pérez L, Arias CA, Rubio R, Haulani L, García Raurich J, Pallarés M, de Pablo J, Morató J. Effect of intermittent induced aeration on nitrogen removal and denitrifying-bacterial community structure in Cork and gravel vertical flow pilot-scale treatment wetlands. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:1121-1130. [PMID: 34415215 DOI: 10.1080/10934529.2021.1967652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
In this work, we have evaluated the impact of intermittent induced aeration in total nitrogen (TN), ammonia (NH4-N) and nitrate-nitrogen (NO3-N) removal in four pilot-scale vertical flow constructed wetlands (VFCW) (two aerated two non-aerated) using cork by-product or gravel as the filter material and planted with Phragmites australis. Both aerated and non-aerated systems achieved high COD and BOD5 elimination rates (≥ 90%) at the end of the 5-month test period. However, the aerated systems presented maximal COD and BOD5 removal from the third month of operation onwards since air supply favored the oxidative bioprocesses occurring within the wetlands. Cork and gravel aerated VFCW also proved to be more efficient (p < 0.05) in NO3-N removal than the non-aerated systems and this upgraded performance was correlated with a significant higher relative abundance of the nirS gene. The aerated systems also showed a slightly improved NH4-N removal. Noticeably, cork VFCW showed higher TN removal mean values (∼35%) than gravel wetlands (27-28%) regardless aeration. Moreover, cork VFCW showed higher relative abundance of the nosZ gene. Our results demonstrated a better nitrogen elimination for the aerated cork pilot-scale VFCW, and this behavior was correlated with a higher abundance of both nirS and nosZ, two of the key functional genes involved in nitrogen metabolism.
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Affiliation(s)
- Lorena Aguilar
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Ángel Gallegos
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Leonardo Martín Pérez
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO-UCA, CONICET), Fac. de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA-Rosario), Rosario (Santa Fe), Argentina
| | - Carlos A Arias
- Department of Biological Sciences, University of Aarhus, Arhus C, Denmark
- Aarhus University Centre for Water Technology WATEC, Aarhus University, Aarhus C, Denmark
| | - Raquel Rubio
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Leila Haulani
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Josep García Raurich
- Centro de Investigación en Seguridad y Control Alimentario (CRESCA), Depto. de Ingeniería Química, Universidad Politécnica de Cataluña-BarcelonaTech, Terrassa, Spain
| | - Marc Pallarés
- Grupo de Desarrollo Empresarial, I + D+i, S.L, C/Colom, Terrassa, Spain
| | - Joan de Pablo
- Resource Recovery and Environmental Management (R2EM), Depto. de Ingeniería Química, Universidad Politécnica de Cataluña-BarcelonaTech, Barcelona, Spain
| | - Jordi Morató
- UNESCO Chair on Sustainability, Universitat Politècnica de Catalunya, Terrassa, Spain
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7
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Cadmium Uptake, MT Gene Activation and Structure of Large-Sized Multi-Domain Metallothioneins in the Terrestrial Door Snail Alinda biplicata (Gastropoda, Clausiliidae). Int J Mol Sci 2020; 21:ijms21051631. [PMID: 32120996 PMCID: PMC7084494 DOI: 10.3390/ijms21051631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Terrestrial snails (Gastropoda) possess Cd-selective metallothioneins (CdMTs) that inactivate Cd2+ with high affinity. Most of these MTs are small Cysteine-rich proteins that bind 6 Cd2+ equivalents within two distinct metal-binding domains, with a binding stoichiometry of 3 Cd2+ ions per domain. Recently, unusually large, so-called multi-domain MTs (md-MTs) were discovered in the terrestrial door snail Alinda biplicata (A.b.). The aim of this study is to evaluate the ability of A.b. to cope with Cd stress and the potential involvement of md-MTs in its detoxification. Snails were exposed to increasing Cd concentrations, and Cd-tissue concentrations were quantified. The gene structure of two md-MTs (9md-MT and 10md-MT) was characterized, and the impact of Cd exposure on MT gene transcription was quantified via qRT PCR. A.b. efficiently accumulates Cd at moderately elevated concentrations in the feed, but avoids food uptake at excessively high Cd levels. The structure and expression of the long md-MT genes of A.b. were characterized. Although both genes are intronless, they are still transcribed, being significantly upregulated upon Cd exposure. Overall, our results contribute new knowledge regarding the metal handling of Alinda biplicata in particular, and the potential role of md-MTs in Cd detoxification of terrestrial snails, in general.
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8
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Codony F, Dinh-Thanh M, Agustí G. Key Factors for Removing Bias in Viability PCR-Based Methods: A Review. Curr Microbiol 2019; 77:682-687. [DOI: 10.1007/s00284-019-01829-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/29/2019] [Indexed: 11/24/2022]
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9
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Martins L, Fernandes C, Albuquerque P, Tavares F. Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR. PLANT DISEASE 2019; 103:2577-2586. [PMID: 31347945 DOI: 10.1094/pdis-12-18-2253-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R2 > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.
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Affiliation(s)
- Leonor Martins
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Camila Fernandes
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras, Portugal
| | - Pedro Albuquerque
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Fernando Tavares
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
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10
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Papaiakovou M, Gasser RB, Littlewood DTJ. Quantitative PCR-Based Diagnosis of Soil-Transmitted Helminth Infections: Faecal or Fickle? Trends Parasitol 2019; 35:491-500. [PMID: 31126720 DOI: 10.1016/j.pt.2019.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/19/2022]
Abstract
Treatment and control programmes tackling soil-transmitted helminth (STH) infections require sensitive, reliable, and accurate diagnostic tools. There is a growing need for measures of infection intensity as programmes approach STH control. Quantitative real-time PCR (qPCR) is well suited to the detection of DNA targets present in stool, even in low-prevalence settings. Detecting low levels of infection becomes increasingly important when the breakpoint of transmission is approached, and is vital when monitoring for recrudescence once control, or possibly 'elimination', is achieved. We address key challenges and questions that remain as barriers to incorporating qPCR as a cornerstone diagnostic tool for STH infections.
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Affiliation(s)
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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11
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Schmielau L, Dvorak M, Niederwanger M, Dobieszewski N, Pedrini-Martha V, Ladurner P, Pedregal JRG, Maréchal JD, Dallinger R. Differential response to Cadmium exposure by expression of a two and a three-domain metallothionein isoform in the land winkle Pomatias elegans: Valuating the marine heritage of a land snail. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:561-571. [PMID: 30121534 DOI: 10.1016/j.scitotenv.2018.07.426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Through evolution, marine snails have adapted several times independently to terrestrial life. A prime example for such transitions is the adaptation to terrestrial conditions in members of the gastropod clade of Littorinoidea (Caenogastropoda). Some species of this lineage like the periwinkle (Littorina littorea), live in intertidal habitats, where they are intermittently exposed to semi-terrestrial conditions. Pomatias elegans is a close relative of Littorina littorea that has successfully colonized terrestrial habitats. Evolutionary transitions from marine to terrestrial conditions have often been fostered in marine ancestors by acquisition of physiological pre-adaptations to terrestrial life. Such pre-adaptations are based, among others, on the optimization of a wide repertoire of stress resistance mechanisms, such as the expression of metal inactivating metallothioneins (MTs). The objective of our study was to explore the Cd handling strategy in the terrestrial snail Pomatias elegans in comparison to that observed previously in Littorina littorea. After Cd exposure, the metal is accumulated mainly in the midgut gland of Pomatias elegans, in a similar way as in its marine relative. Upon Cd exposure, Pomatias elegans expresses Cd-specific MTs, as also described from Littorina littorea. In contrast to the latter species, however, the detoxification of Cd in Pomatias elegans is mediated by two different MT isoforms, one two-domain and one three-domain MT. Although the MT proteins of both species are homologous and clearly originate from one common ancestor, the three-domain MT isoform of Pomatias elegans has evolved independently from the three-domain MT of its marine counterpart, probably by addition of a third domain to the pre-existing two-domain MT. Obviously, the occurrence of homologous MT structures in both species is a hereditary character, whereas the differentiation into two distinct MT isoforms with different upregulation capacities in Pomatias elegans is an adaptive feature that probably emerged upon transition to life on land.
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Affiliation(s)
- Lara Schmielau
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martin Dvorak
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Michael Niederwanger
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Nicole Dobieszewski
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Veronika Pedrini-Martha
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Peter Ladurner
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | | | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Reinhard Dallinger
- Department of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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12
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Egeter B, Peixoto S, Brito JC, Jarman S, Puppo P, Velo-Antón G. Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA. Genome 2018; 61:807-814. [DOI: 10.1139/gen-2018-0071] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.
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Affiliation(s)
- Bastian Egeter
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Sara Peixoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - José C. Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, Molecular and Life Sciences, Curtin University, WA, 6102, Australia
- Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, 6009, Australia
| | - Pamela Puppo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
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Bonk F, Popp D, Harms H, Centler F. PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. J Microbiol Methods 2018; 153:139-147. [DOI: 10.1016/j.mimet.2018.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/25/2022]
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14
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Schneebauer G, Mauracher D, Fiechtner B, Pelster B. Transcript levels of members of the SLC2 and SLC5 families of glucose transport proteins in eel swimbladder tissue: the influence of silvering and the influence of a nematode infection. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:599-613. [PMID: 29327317 PMCID: PMC5862955 DOI: 10.1007/s10695-017-0456-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
The rate of glucose metabolism has been shown to be correlated to glucose uptake in swimbladder gas gland cells. Therefore, it is assumed that in the European eel silvering, i.e., the preparation of the eel for the spawning migration to the Sargasso Sea, coincides with an enhanced capacity for glucose uptake. To test this hypothesis expression of all known glucose transport proteins has been assessed at the transcript level in yellow and in silver eels, and we also included Anguillicola crassus infected swimbladders. Glucose uptake by rete mirabile endothelial cells could be crucial for the countercurrent exchange capacity of the rete. Therefore, this tissue was also included in our analysis. The results revealed expression of ten different members of the slc2 family of glucose transporters, of four slc5 family members, and of kiaa1919 in gas gland tissue. Glucose transporters of the slc2 family were expressed at very high level, and slc2a1b made up about 80% of all slc2 family members, irrespective of the developmental state or the infection status of the eel. Overall, the slc5 family contributed to only about 8% of all detected glucose transport transcripts in gas gland tissue, and the slc2 family to more than 85%. In rete capillaries, the contribution of sodium-dependent glucose transporters was significantly higher, leaving only 66% for the slc2 family of glucose transporters. Neither silvering nor the infection status had a significant effect on the expression of glucose transporters in swimbladder gas gland tissue, suggesting that glucose metabolism of eel gas gland cells may not be related to transcriptional changes of glucose transport proteins.
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Affiliation(s)
- Gabriel Schneebauer
- Institute of Zoology, Leopold-Franzens-Universität Innsbruck, Technikerstr.25, 6020, Innsbruck, Austria
- Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - David Mauracher
- Institute of Zoology, Leopold-Franzens-Universität Innsbruck, Technikerstr.25, 6020, Innsbruck, Austria
- Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Birgit Fiechtner
- Institute of Zoology, Leopold-Franzens-Universität Innsbruck, Technikerstr.25, 6020, Innsbruck, Austria
- Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Bernd Pelster
- Institute of Zoology, Leopold-Franzens-Universität Innsbruck, Technikerstr.25, 6020, Innsbruck, Austria.
- Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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15
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Stewart K, Ma H, Zheng J, Zhao J. Using environmental DNA to assess population-wide spatiotemporal reserve use. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2017; 31:1173-1182. [PMID: 28221696 DOI: 10.1111/cobi.12910] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Scientists increasingly rely on protected areas to assist in biodiversity conservation, yet the efficacy of these areas is rarely systematically assessed, often because of underfunding. Still, adaptive management strategies to maximize conservation success often rely on understanding the temporal and spatial dynamism of populations therein. Examination of environmental DNA (eDNA) is a time and cost-effective way to monitor species' distribution, and quantitative polymerase chain reaction (qPCR) provides information on organismal abundance. To date, however, such techniques remain underused for population assessments in protected areas. We determined eDNA concentration of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to describe its occurrence, range, and use of the Tian e-Zhou National Nature Reserve in Hubei, China, across seasons and hydrological depths. Despite the observation that total eDNA concentrations were highest in surface waters in summer, finless porpoise eDNA concentrations were significantly higher in deeper waters than in surface waters in summer. During the breeding season (spring), eDNA signals were site specific and restricted to the core area of the reserve. However, postbreeding eDNA concentrations were widespread across the reserve, encompassing sites previously thought to be unfrequented by the species. Our results suggest spatiotemporal idiosyncrasies in site, depth, and seasonal use of the reserve and a propensity for postbreeding population dispersal. With eDNA and qPCR we were able to assess an entire population's use of a protected area. Illuminating nuances in habitat use via eDNA could be valuable to set pragmatic conservation goals for this, and other, species.
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Affiliation(s)
- Kathryn Stewart
- College of Environmental Science and Engineering, Tongji University, Shanghai, P.R. China
| | - Hongjuan Ma
- College of Environmental Science and Engineering, Tongji University, Shanghai, P.R. China
| | - Jinsong Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Jianfu Zhao
- College of Environmental Science and Engineering, Tongji University, Shanghai, P.R. China
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16
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Pedrini-Martha V, Schnegg R, Baurand PE, deVaufleury A, Dallinger R. The physiological role and toxicological significance of the non-metal-selective cadmium/copper-metallothionein isoform differ between embryonic and adult helicid snails. Comp Biochem Physiol C Toxicol Pharmacol 2017; 199:38-47. [PMID: 28254493 DOI: 10.1016/j.cbpc.2017.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 11/20/2022]
Abstract
Metal regulation is essential for terrestrial gastropods to survive. In helicid snails, two metal-selective metallothionein (MT) isoforms with different functions are expressed. A cadmium-selective isoform (CdMT) plays a major role in Cd2+ detoxification and stress response, whereas a copper-selective MT (CuMT) is involved in Cu homeostasis and hemocyanin synthesis. A third, non-metal-selective isoform, called Cd/CuMT, was first characterized in Cantareus aspersus. The aim of this study was to quantify the transcriptional activity of all three MT genes in unexposed and metal-exposed (Cd, Cu) embryonic Roman snails. In addition, the complete Cd/CuMT mRNA of the Roman snail (Helix pomatia) was characterized, and its expression quantified in unexposed and Cd-treated adult individuals. In embryos of Helix pomatia, the Cd/CuMT gene was induced upon Cu exposure. Its transcription levels were many times higher than that of the other two MT genes, and also exceeded by far the Cd/CuMT mRNA concentrations of adult snails. In the hepatopancreas of adult Roman snails, no Cd/CuMT could be detected at the protein level, irrespective of whether the snails had been exposed to Cd or not. This contrasts with the situation in the near relative, Cantareus aspersus. It appeared that the 3'-UTR of the Cd/CuMT mRNA differed largely between Cantareus aspersus and Helix pomatia, being larger in the latter species, with a number of putative binding sites for proteins and miRNAs known to inhibit mRNA translation. We suggest this as a possible mechanism responsible for the lack of Cd/CuMT protein expression in adult Roman snails.
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Affiliation(s)
| | - Raimund Schnegg
- Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Pierre-Emmanuel Baurand
- Chrono-Environnement, UMR 6249 University of Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| | - Annette deVaufleury
- Chrono-Environnement, UMR 6249 University of Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France; Department of Health Safety Environment, avenue des Rives du Lac, BP179, 70003 Vesoul cedex, France
| | - Reinhard Dallinger
- Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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17
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Baebler Š, Svalina M, Petek M, Stare K, Rotter A, Pompe-Novak M, Gruden K. quantGenius: implementation of a decision support system for qPCR-based gene quantification. BMC Bioinformatics 2017; 18:276. [PMID: 28545393 PMCID: PMC5445471 DOI: 10.1186/s12859-017-1688-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/16/2017] [Indexed: 12/21/2022] Open
Abstract
Background Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. Results We have developed “quantGenius” (http://quantgenius.nib.si), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry–independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. Conclusions To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1688-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia.
| | - Miha Svalina
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Ana Rotter
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Maruša Pompe-Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, SI, Slovenia
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18
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Cattani F, Barth VC, Nasário JSR, Ferreira CAS, Oliveira SD. Detection and quantification of viable Bacillus cereus group species in milk by propidium monoazide quantitative real-time PCR. J Dairy Sci 2016; 99:2617-2624. [PMID: 26830746 DOI: 10.3168/jds.2015-10019] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022]
Abstract
The Bacillus cereus group includes important spore-forming bacteria that present spoilage capability and may cause foodborne diseases. These microorganisms are traditionally evaluated in food using culturing methods, which can be laborious and time-consuming, and may also fail to detect bacteria in a viable but nonculturable state. The purpose of this study was to develop a quantitative real-time PCR (qPCR) combined with a propidium monoazide (PMA) treatment to analyze the contamination of UHT milk by B. cereus group species viable cells. Thirty micrograms per milliliter of PMA was shown to be the most effective concentration for reducing the PCR amplification of extracellular DNA and DNA from dead cells. The quantification limit of the PMA-qPCR assay was 7.5 × 10(2) cfu/mL of milk. One hundred thirty-five UHT milk samples were analyzed to evaluate the association of PMA to qPCR to selectively detect viable cells. The PMA-qPCR was able to detect B. cereus group species in 44 samples (32.6%), whereas qPCR without PMA detected 78 positive samples (57.8%). Therefore, the PMA probably inhibited the amplification of DNA from cells that were killed during UHT processing, which avoided an overestimation of bacterial cells when using qPCR and, thus, did not overvalue potential health risks. A culture-based method was also used to detect and quantify B. cereus sensu stricto in the same samples and showed positive results in 15 (11.1%) samples. The culture method and PMA-qPCR allowed the detection of B. cereus sensu stricto in quantities compatible with the infective dose required to cause foodborne disease in 3 samples, indicating that, depending on the storage conditions, even after UHT treatment, infective doses may be reached in ready-to-consume products.
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Affiliation(s)
- Fernanda Cattani
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brazil
| | - Valdir C Barth
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brazil
| | - Jéssica S R Nasário
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brazil
| | - Carlos A S Ferreira
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brazil
| | - Sílvia D Oliveira
- Laboratório de Imunologia e Microbiologia, Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brazil.
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Urubschurov V, Büsing K, Janczyk P, Souffrant WB, Zeyner A. Development and Evaluation of qPCR Assay for Quantitation of Kazachstania slooffiae and Total Yeasts Occurring in the Porcine Gut. Curr Microbiol 2015; 71:373-81. [PMID: 26134536 DOI: 10.1007/s00284-015-0862-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
Abstract
Kazachstania slooffiae is the dominating yeast in pig's gut. No methods others than cultivation were applied for enumeration of yeasts within this ecosystem. Therefore, the aim of this study was to develop a real-time quantitative polymerase chain reaction (qPCR) assay to quantitate total yeasts and K. slooffiae in the porcine gut. This work demonstrated that the copy numbers in gDNA can be determined by qPCR using PCR amplicons as a calibrator and one-point calibration method. The gDNA were then used as a calibrator for further analysis. The values of quantitation cycle and PCR amplification efficiency of gDNA calibrator were highly reproducible. DNA was extracted from feces and from 10 different cultured yeasts found in pigs' intestine. The qPCR results using primers NL1/LS2 encoding 26S rDNA correlated (r = 0.984, P < 0.0001) with cultivation results. From two primer sets developed, one set encoding act1 gene was suitable for quantitation of K. slooffiae. The copy numbers of K. slooffiae could be determined by 40% analyzed animals, amounting to about 70% of total yeasts. The application of this method in next studies will help to get more information about K. slooffiae and total yeasts in the gut of pigs.
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Affiliation(s)
- Vladimir Urubschurov
- Institute of Agricultural and Nutritional Sciences, Group Animal Nutrition, Martin Luther University Halle-Wittenberg, Theodor-Lieser-Straße 11, 06120, Halle (Saale), Germany,
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