1
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Cold-tolerant microorganisms causing spoilage of vacuum-packed beef under time-temperature abuse determined by culture and qPCR. Food Microbiol 2023; 109:104147. [DOI: 10.1016/j.fm.2022.104147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022]
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2
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Cai W, Wang Y, Liu Z, Liu J, Zhong J, Hou Q, Yang X, Shan C, Guo Z. Depth-depended quality comparison of light-flavor fermented grains from two fermentation rounds. Food Res Int 2022; 159:111587. [DOI: 10.1016/j.foodres.2022.111587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/13/2022]
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3
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Zwirzitz B, Thalguter S, Wetzels SU, Stessl B, Wagner M, Selberherr E. Autochthonous fungi are central components in microbial community structure in raw fermented sausages. Microb Biotechnol 2021; 15:1392-1403. [PMID: 34739743 PMCID: PMC9049617 DOI: 10.1111/1751-7915.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Raw meat sausage represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. Starter cultures are applied to improve product stability and safety as well as flavour characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not yet been explored. We evaluate the microbiological status of four different raw meat sausages using high‐throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to the starter culture Lactobacillus sakei and the spoilage‐associated genera Acinetobacter, Pseudomonas and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Stefanie U Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
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4
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Hu Y, Lei X, Zhang X, Guan T, Wang L, Zhang Z, Yu X, Tu J, Peng N, Liang Y, Zhao S. Characteristics of the Microbial Community in the Production of Chinese Rice-Flavor Baijiu and Comparisons With the Microflora of Other Flavors of Baijiu. Front Microbiol 2021; 12:673670. [PMID: 33995338 PMCID: PMC8116502 DOI: 10.3389/fmicb.2021.673670] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Rice-flavor baijiu is one of the four basic flavor types of Chinese baijiu. Microbial composition plays a key role in the classification of baijiu flavor types and the formation of flavor substances. In this study, we used high-throughput sequencing technology to study the changes of microbial community in the production of rice-flavor baijiu, and compared the microbial community characteristics during production of rice-, light-, and strong-flavor baijiu. The results showed that the species diversity of bacteria was much higher than that of fungi during the brewing of rice-flavor baijiu. The bacterial diversity index first increased and then decreased, while the diversity of fungi showed an increasing trend. A variety of major microorganisms came from the environment and raw rice materials; the core bacteria were Lactobacillus, Weissella, Pediococcus, Lactococcus, Acetobacter, etc., among which Lactobacillus was dominant (62.88-99.23%). The core fungi were Saccharomyces (7.06-83.50%) and Rhizopus (15.21-90.89%). Temperature and total acid content were the main physicochemical factors affecting the microbial composition. Non-metric multidimensional scaling analysis showed that during the fermentation of rice-, light-, and strong-flavor baijiu, their microbial communities formed their own distinct systems, with considerable differences among different flavor types. Compared with the other two flavor types of baijiu, in the brewing process of rice-flavor baijiu, microbial species were fewer and dominant microorganisms were prominent, which may be the main reason for the small variety of flavor substances in rice-flavor baijiu. This study provides a theoretical basis for the production of rice-flavor baijiu, and lays a foundation for studying the link between baijiu flavor formation and microorganisms.
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Affiliation(s)
- Yuanliang Hu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Engineering Research Center of Typical Wild Vegetable Breeding and Comprehensive Utilization Technology, Huangshi, China
| | - Xinyi Lei
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Xiaomin Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guangdong Deqing Incomparable Health Wine Co., Ltd., Zhaoqing, China
| | - Tongwei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Luyao Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Zongjie Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Xiang Yu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Junming Tu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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5
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The potential correlations between the fungal communities and volatile compounds of traditional dry sausages from Northeast China. Food Microbiol 2021; 98:103787. [PMID: 33875215 DOI: 10.1016/j.fm.2021.103787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/12/2021] [Accepted: 03/08/2021] [Indexed: 11/21/2022]
Abstract
The fungal communities and volatile compounds of traditional dry sausages collected from five different regions in Northeast China, including Harbin (HRB), Daqing (DQ), Suihua (SH), Hegang (HG) and Mudanjiang (MDJ) were investigated in this study. The results revealed clear differences among the fungal community structures of the sausages. Aspergillus pseudoglaucus, Debaryomyces hansenii, and Trichosporon asahii were found to be the predominant species in the sausages from HRB, HG, and MDJ, respectively. Candida zeylanoides was the predominant species in the sausage from DQ and SH. Additionally, 88 volatile compounds were identified in all sausages, of which 31 volatile compounds were the most important flavor contributors (odor activity value > 1). Potential correlation analysis revealed that 8 fungi (D. hansenii, C. zeylanoides, T. asahii, A. pseudoglaucus, Aspergillus sydowii, Penicillium expansum, A. alternata, and Alternaria tenuissima) showed significant positive correlations with ≥3 key volatile compounds. Among these fungi, D. hansenii was regarded as a core functional fungus responsible for the formation of the volatile compounds, given its strong connection with the highest number of key volatile compounds. These results provide detailed insight into the fungal communities of traditional dry sausages and a deeper understanding of the contribution of these fungi to sausage flavor.
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6
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Predominant yeasts in Chinese Dong fermented pork (Nanx Wudl) and their aroma-producing properties in fermented sausage condition. FOOD SCIENCE AND HUMAN WELLNESS 2021. [DOI: 10.1016/j.fshw.2021.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Wen R, Li XA, Han G, Chen Q, Kong B. Fungal community succession and volatile compound dynamics in Harbin dry sausage during fermentation. Food Microbiol 2021; 99:103764. [PMID: 34119122 DOI: 10.1016/j.fm.2021.103764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/27/2022]
Abstract
This study investigated the fungal community succession and volatile compound dynamics of Harbin dry sausage during a twelve-day fermentation using high-throughput internal transcribed spacer amplicon sequencing and headspace solid-phase microextraction gas chromatography-mass spectrometry. Aspergillus pseudoglaucus was found to be the primary species in the sausages during fermentation, whereas Lasiodiplodia theobromae, Alternaria alternata, Aspergillus caesiellus, and Trichosporon asahii were also prevalent. Additionally, a total of 72 volatile compounds were identified in the dry sausages, of which 24 key compounds (odor activity value > 1) dominated flavor development, including 3 aldehydes, 1 ketone, 4 alcohols, 9 esters, 4 alkenes, and 3 other compounds. Furthermore, correlation analysis suggested that most of the core fungi were positively correlated with the key volatile compounds, particularly A. pseudoglaucus, Aspergillus gracilis, Trichosporon caseorum, Debaryomyces hansenii, and T. asahii. Our findings provide novel insights into the fungal ecology and flavor development of Harbin dry sausages.
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Affiliation(s)
- Rongxin Wen
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Xiang-Ao Li
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Ge Han
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Qian Chen
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
| | - Baohua Kong
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
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8
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Floc'h JB, Hamel C, Harker KN, St-Arnaud M. Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome. MICROBIAL ECOLOGY 2020; 80:762-777. [PMID: 31897569 DOI: 10.1007/s00248-019-01475-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/16/2019] [Indexed: 05/25/2023]
Abstract
Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.
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Affiliation(s)
- Jean-Baptiste Floc'h
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - K Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada.
- Jardin Botanique de Montréal, Montreal, Canada.
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9
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Belleggia L, Ferrocino I, Reale A, Boscaino F, Di Renzo T, Corvaglia MR, Cocolin L, Milanović V, Cardinali F, Garofalo C, Clementi F, Aquilanti L, Osimani A. Portuguese cacholeira blood sausage: A first taste of its microbiota and volatile organic compounds. Food Res Int 2020; 136:109567. [DOI: 10.1016/j.foodres.2020.109567] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 12/29/2022]
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10
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Dharampal PS, Diaz-Garcia L, Haase MAB, Zalapa J, Currie CR, Hittinger CT, Steffan SA. Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies. INSECTS 2020; 11:insects11040250. [PMID: 32316296 PMCID: PMC7240610 DOI: 10.3390/insects11040250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/14/2022]
Abstract
The pollen stores of bumble bees host diverse microbiota that influence overall colony fitness. Yet, the taxonomic identity of these symbiotic microbes is relatively unknown. In this descriptive study, we characterized the microbial community of pollen provisions within captive-bred bumble bee hives obtained from two commercial suppliers located in North America. Findings from 16S rRNA and ITS gene-based analyses revealed that pollen provisions from the captive-bred hives shared several microbial taxa that have been previously detected among wild populations. While diverse microbes across phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Ascomycota were detected in all commercial hives, significant differences were detected at finer-scale taxonomic resolution based on the supplier source. The causative agent of chalkbrood disease in honey bees, Ascosphaera apis, was detected in all hives obtained from one supplier source, although none of the hives showed symptoms of infection. The shared core microbiota across both commercial supplier sources consisted of two ubiquitous bee-associated groups, Lactobacillus and Wickerhamiella/Starmerella clade yeasts that potentially contribute to the beneficial function of the microbiome of bumble bee pollen provisions.
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Affiliation(s)
- Prarthana S. Dharampal
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence:
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Aguascalientes 20676, Mexico
| | - Max A. B. Haase
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; (L.D.-G.); (J.Z.)
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.A.B.H.); (C.T.H.)
| | - Shawn A. Steffan
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA;
- USDA-ARS, Vegetable Crop Research Unit, Madison, WI 53706, USA
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11
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Nondestructive Detection Method for Beef Water-Holding Capacity Using Modified Test Paper. INTERNATIONAL JOURNAL OF FOOD ENGINEERING 2019. [DOI: 10.1515/ijfe-2018-0396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWater-holding capacity (WHC) is a critical indicator of beef quality. Several conventional test methods have high cost or spend more time. In this study, a rapid detection method was developed to measure WHC by modified test paper. The test paper was modified by cobalt chloride for its color turned from blue to red after contacting with water. When the test paper was attached to the surface of meat sample, its color would change. The time of color changing was related to WHC. A prediction model was built. The prediction accuracy was 90 % and the detection time was less than 1 min. The results of scanning electron microscope (SEM) analysis showed that the three-dimensional network structures of the test paper were more compact and homogeneous. Accordingly, the modified test paper exhibits a more stable property and can be used for other meat products.
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12
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Dollhofer V, Dandikas V, Dorn-In S, Bauer C, Lebuhn M, Bauer J. Accelerated biogas production from lignocellulosic biomass after pre-treatment with Neocallimastix frontalis. BIORESOURCE TECHNOLOGY 2018; 264:219-227. [PMID: 29807329 DOI: 10.1016/j.biortech.2018.05.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Two Neocallimastix frontalis strains, isolated from rumen fluid of a cow and of a chamois, were assessed for their ability to degrade lignocellulosic biomass. Two independent batch experiments were performed. Each experiment was split into two phases: hydrolysis phase and batch fermentation phase. The hydrolysis process during the N. frontalis incubation led to an initial increase of biogas production, an accelerated degradation of dry matter and an increased concentration of volatile fatty acids. As monitored by quantitative PCR, the applied N. frontalis strains were present and transcriptionally active during the hydrolysis phase but were fading during the batch fermentation phase. Thus, a separate hydrolytic pretreatment phase with anaerobic fungi, such as N. frontalis, represents a feasible strategy to improve biogas production from lignocellulosic substrates.
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Affiliation(s)
- Veronika Dollhofer
- Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany.
| | - Vasilis Dandikas
- Institute for Agricultural Engineering and Animal Husbandry, Bavarian State Research Center for Agriculture, Am Staudengarten 3, 85354 Freising, Germany
| | - Samart Dorn-In
- School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Christoph Bauer
- Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Michael Lebuhn
- Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Johann Bauer
- School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
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13
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Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT. Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health. J Vis Exp 2017. [PMID: 29053686 DOI: 10.3791/54631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.
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Affiliation(s)
- Shawn A Steffan
- Vegetable Crop Research Unit, USDA-ARS; Department of Entomology, University of Wisconsin-Madison;
| | | | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin-Madison; Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias
| | | | - Juan Zalapa
- Vegetable Crop Research Unit, USDA-ARS; Department of Horticulture, University of Wisconsin-Madison
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin; DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
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14
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Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA. J Microbiol Methods 2015; 113:50-6. [PMID: 25863142 DOI: 10.1016/j.mimet.2015.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/07/2015] [Accepted: 04/07/2015] [Indexed: 01/19/2023]
Abstract
Universal primers targeting the bacterial 16S-rRNA-gene allow quantification of the total bacterial load in variable sample types by qPCR. However, many universal primer pairs also amplify DNA of plants or even of archaea and other eukaryotic cells. By using these primers, the total bacterial load might be misevaluated, whenever samples contain high amounts of non-target DNA. Thus, this study aimed to provide primer pairs which are suitable for quantification and identification of bacterial DNA in samples such as feed, spices and sample material from digesters. For 42 primers, mismatches to the sequence of chloroplasts and mitochondria of plants were evaluated. Six primer pairs were further analyzed with regard to the question whether they anneal to DNA of archaea, animal tissue and fungi. Subsequently they were tested with sample matrix such as plants, feed, feces, soil and environmental samples. To this purpose, the target DNA in the samples was quantified by qPCR. The PCR products of plant and feed samples were further processed for the Single Strand Conformation Polymorphism method followed by sequence analysis. The sequencing results revealed that primer pair 335F/769R amplified only bacterial DNA in samples such as plants and animal feed, in which the DNA of plants prevailed.
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15
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Nasser LA. Molecular identification of isolated fungi, microbial and heavy metal contamination of canned meat products sold in Riyadh, Saudi Arabia. Saudi J Biol Sci 2014; 22:513-20. [PMID: 26288552 PMCID: PMC4537861 DOI: 10.1016/j.sjbs.2014.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/11/2014] [Accepted: 08/24/2014] [Indexed: 11/21/2022] Open
Abstract
Several studies have shown that canned meat products may be contaminated with fungal elements, bacteria and even heavy metals which may occur during the transportation, storage and handling processes. We conducted this study to determine the fungal, microbial and heavy metal contents of canned meats in Saudi Arabia. Of the 13 canned meat samples studied, Aspergillus and Penicillium were found in more than 70% of the total samples. Sequences of Penicillium species isolated from meat samples generated a phylogenetic tree which shows that the studied isolates were clustered in four groups. No bacterial contamination was noted in all of the samples. Nine of the 13 samples had iron concentrations above the permissible limit. All samples had zinc and copper levels below the maximum permissible limit. Four samples had cadmium levels above the maximum permissible level. All samples had levels of lead above the maximum permissible levels. These results indicate that fungal elements and higher levels of heavy metals such as lead and cadmium can be found in canned meat products. This may pose as a real danger to consumers, since canned meat products are readily accessible and convenient in Saudi Arabia.
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Affiliation(s)
- Laila A Nasser
- College of Science, Biology Department, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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16
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Dorn-In S, Fahn C, Hölzel CS, Wenz S, Hartwig I, Schwaiger K, Bauer J. Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR. FEMS Microbiol Lett 2014; 359:182-92. [PMID: 25088501 DOI: 10.1111/1574-6968.12552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/30/2014] [Accepted: 07/30/2014] [Indexed: 11/28/2022] Open
Abstract
Ground feeds for pigs were investigated for fungal contamination before and after pelleting (subsamples in total n = 24) by cultural and molecular biological methods. A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. Twenty-two DNA bands were sequenced; all represented fungal DNA. The level of fungal DNA in ground feed samples was equivalent to 4.77-5.69 log10 CFU g(-1) , calculated by qPCR using a standard curve of Aspergillus flavus. In pelleted feed, the level of fungal DNA was in average ± 0.07 log10 different from ground feed. Quantified by cultural methods, the fresh ground feeds contained up to 4.51 log10 CFU g(-1) culturable fungi, while there was < 2.83 log10 CFU g(-1) detected in pelleted feeds. This result shows that, while the process of pelleting reduced the amount of living fungi dramatically, it did not affect the total fungal DNA in feed. Thus, the described methodology was able to reconstruct the fungal microbiota in feeds and reflected a considerable fungal contamination of raw materials such as grains.
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Janke T, Schwaiger K, Ege M, Fahn C, von Mutius E, Bauer J, Mayer M. Analysis of the Fungal Flora in Environmental Dust Samples by PCR–SSCP Method. Curr Microbiol 2013; 67:156-69. [DOI: 10.1007/s00284-013-0344-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
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