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Bruno A, Sandionigi A, Panio A, Rimoldi S, Orizio F, Agostinetto G, Hasan I, Gasco L, Terova G, Labra M. Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets. BMC Microbiol 2023; 23:248. [PMID: 37674159 PMCID: PMC10481543 DOI: 10.1186/s12866-023-02990-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples. RESULTS Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group. CONCLUSIONS Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy.
| | | | - Antonella Panio
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Milan, Italy
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavio Orizio
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
| | - Giulia Agostinetto
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
| | - Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Torino, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Massimo Labra
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
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2
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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3
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Dynamic analysis of physicochemical characteristics and microbial communities of Aspergillus-type douchi during fermentation. Food Res Int 2022; 153:110932. [DOI: 10.1016/j.foodres.2021.110932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/19/2021] [Accepted: 12/28/2021] [Indexed: 11/20/2022]
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4
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Caron K, Craw P, Richardson MB, Bodrossy L, Voelcker NH, Thissen H, Sutherland TD. The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance. SENSORS 2021; 21:s21196625. [PMID: 34640944 PMCID: PMC8513014 DOI: 10.3390/s21196625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.
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Affiliation(s)
- Karine Caron
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
| | - Pascal Craw
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Mark B. Richardson
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Levente Bodrossy
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Nicolas H. Voelcker
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Tara D. Sutherland
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
- Correspondence:
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5
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Wang Y, Xiang F, Zhang Z, Hou Q, Guo Z. Characterization of bacterial community and flavor differences of different types of Douchi. Food Sci Nutr 2021; 9:3460-3469. [PMID: 34262706 PMCID: PMC8269581 DOI: 10.1002/fsn3.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
According to the appearance and technology, traditional fermented Douchi can be divided into dried Douchi and wet Douchi. However, there are few reports on the difference of bacterial community structure between them or the influence of bacterial community on product flavor. In this study, high-throughput sequencing technology and electronic nose were used to measure the bacterial diversity and flavor of 40 Douchi samples, and the correlation between them was explored by multivariate statistical means combined with COG database. Results showed that the cumulative average relative abundance of Firmicutes and Proteobacteria in the samples was as high as 95.93%, and the former was the core bacteria phylum. On the whole, the dominant bacteria in Douchi were Bacillus (50.67%), Staphylococcus (14.07%), Enterococcus (2.54%), Proteus (1.61%), Brevibacillus (1.46%), Providencia (1.26%), Weissella (1.24%), and Ureibacillus (1.19%). LEfSe analysis indicated that Bacillus can be used as a biomarker in dried fermented soybeans. Meanwhile, dried samples contained more intensive aromatic substances, but were significantly lower in W6S (selectivity to hydrogen) and W3S (methane-aliph) compared with the wet samples. Aneurinibacillus and Brevibacillus were helpful to the formation of aromatic flavor in Douchi, but Vagococcus and Corynebacterium were the opposite. Gene and microbial phenotypic prediction showed that microorganisms in dried Douchi use protein more efficiently, while in wet Douchi, microbial energy metabolism was more vigorous. The pathogenic potential of microorganisms in dried samples was higher than that in wet. This study can sound the alarm for improving the safety of home-brewed Douchi and provide guidance for the subsequent screening of strains that enhance the flavor of fermented soybeans.
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Affiliation(s)
- Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Fanshu Xiang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
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6
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Wang Y, Cai W, Wang W, Shu N, Zhang Z, Hou Q, Shan C, Guo Z. Analysis of microbial diversity and functional differences in different types of high-temperature Daqu. Food Sci Nutr 2021; 9:1003-1016. [PMID: 33598183 PMCID: PMC7866569 DOI: 10.1002/fsn3.2068] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/07/2020] [Accepted: 12/02/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial communities that enrich in high-temperature Daqu are important for the Chinese maotai-flavor liquor brewing process. However, the bacterial communities in three different types of high-temperature Daqu (white Daqu, black Daqu, and yellow Daqu) are still undercharacterized. In this study, the bacterial diversity of three different types of high-temperature Daqu was investigated using Illumina MiSeq high-throughput sequencing. The bacterial community of high-temperature Daqu is mainly composed of thermophilic bacteria, and seven bacterial phyla along with 262 bacterial genera were identified in all 30 high-temperature Daqu samples. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the dominant bacterial phyla in high-temperature Daqu samples, while Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. The bacterial community structure of three different types of high-temperature Daqu was significantly different (p < .05). In addition, the results of microbiome phenotype prediction by BugBase and bacterial functional potential prediction using PICRUSt show that bacteria from different types of high-temperature Daqu have similar functions as well as phenotypes, and bacteria in high-temperature Daqu have vigorous metabolism in the transport and decomposition of amino acids and carbohydrates. These results offer a reference for the comprehensive understanding of bacterial diversity of high-temperature Daqu.
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Affiliation(s)
- Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
- School of Food ScienceShihezi UniversityShiheziChina
| | - Wenping Wang
- Hubei Yaozhihe Chuwengquan Liquor Industry Co., Ltd.XiangyangChina
| | - Na Shu
- Hubei Yaozhihe Chuwengquan Liquor Industry Co., Ltd.XiangyangChina
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Chunhui Shan
- School of Food ScienceShihezi UniversityShiheziChina
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
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7
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Scolari F, Sandionigi A, Carlassara M, Bruno A, Casiraghi M, Bonizzoni M. Exploring Changes in the Microbiota of Aedes albopictus: Comparison Among Breeding Site Water, Larvae, and Adults. Front Microbiol 2021; 12:624170. [PMID: 33584626 PMCID: PMC7876458 DOI: 10.3389/fmicb.2021.624170] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
The mosquito body hosts highly diverse microbes, which influence different physiological traits of both larvae and adults. The composition of adult mosquito microbiota is tightly linked to that of larvae, which are aquatic and feed on organic detritus, algae and prokaryotic microorganisms present in their breeding sites. Unraveling the ecological features of larval habitats that shape the structure of bacterial communities and their interactions with the mosquito host is still a poorly investigated topic in the Asian tiger mosquito Aedes albopictus, a highly invasive species that is vector of numerous arboviruses, including Dengue, Chikungunya, and Zika viruses. In this study, we investigated the composition of the bacterial community present in the water from a natural larval breeding site in which we separately reared wild-collected larvae and hatched eggs of the Foshan reference laboratory strain. Using sequence analysis of bacterial 16S rRNA gene amplicons, we comparatively analyzed the microbiota of the larvae and that of adult mosquitoes, deriving information about the relative impact of the breeding site water on shaping mosquito microbiota. We observed a higher bacterial diversity in breeding site water than in larvae or adults, irrespective of the origin of the sample. Moreover, larvae displayed a significantly different and most diversified microbial community than newly emerged adults, which appeared to be dominated by Proteobacteria. The microbiota of breeding site water significantly increased its diversity over time, suggesting the presence of a dynamic interaction among bacterial communities, breeding sites and mosquito hosts. The analysis of Wolbachia prevalence in adults from Foshan and five additional strains with different geographic origins confirmed the described pattern of dual wAlbA and wAlbB strain infection. However, differences in Wolbachia prevalence were detected, with one strain from La Reunion Island showing up to 18% uninfected individuals. These findings contribute in further understanding the dynamic interactions between the ecology of larval habitats and the structure of host microbiota, as well as providing additional information relative to the patterns of Wolbachia infection.
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Affiliation(s)
- Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Anna Sandionigi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Martina Carlassara
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Antonia Bruno
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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8
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Scolari F, Casiraghi M, Bonizzoni M. Aedes spp. and Their Microbiota: A Review. Front Microbiol 2019; 10:2036. [PMID: 31551973 PMCID: PMC6738348 DOI: 10.3389/fmicb.2019.02036] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Aedes spp. are a major public health concern due to their ability to be efficient vectors of dengue, Chikungunya, Zika, and other arboviruses. With limited vaccines available and no effective therapeutic treatments against arboviruses, the control of Aedes spp. populations is currently the only strategy to prevent disease transmission. Host-associated microbes (i.e., microbiota) recently emerged as a promising field to be explored for novel environmentally friendly vector control strategies. In particular, gut microbiota is revealing its impact on multiple aspects of Aedes spp. biology, including vector competence, thus being a promising target for manipulation. Here we describe the technological advances, which are currently expanding our understanding of microbiota composition, abundance, variability, and function in the two main arboviral vectors, the mosquitoes Aedes aegypti and Aedes albopictus. Aedes spp. microbiota is described in light of its tight connections with the environment, with which mosquitoes interact during their various developmental stages. Unraveling the dynamic interactions among the ecology of the habitat, the mosquito and the microbiota have the potential to uncover novel physiological interdependencies and provide a novel perspective for mosquito control.
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Affiliation(s)
- Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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9
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Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques. Sci Rep 2019; 9:5259. [PMID: 30918268 PMCID: PMC6437164 DOI: 10.1038/s41598-019-40977-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/26/2019] [Indexed: 01/22/2023] Open
Abstract
To inform management and conservation decisions, environmental DNA (eDNA) methods are used to detect genetic material shed into the water by imperiled and invasive species. Methodological enhancements are needed to reduce filter clogging, PCR inhibition, and false-negative detections when eDNA is at low concentrations. In the first of three simple experiments, we sought to ameliorate filter clogging from particulates and organic material through a scaled-up, multi-filter protocol. We combined four filters in a 5 mL Phenol-Chloroform-Isoamyl (PCI) procedure to allow for larger volumes of water (~1 L) to be filtered rapidly. Increasing the filtered water volume by four times resulted in 4.4X the yield of target DNA. Next, inhibition from organic material can reduce or block eDNA detections in PCR-based assays. To remove inhibitory compounds retained during eDNA isolation, we tested three methods to chemically strip inhibitors from eDNA molecules. The use of CTAB as a short-term (5–8 day) storage buffer, followed by a PCI isolation, resulted in the highest eDNA yields. Finally, as opposed to a linear relationship among increasing concentrations of filtered genomic eDNA, we observed a sharp change between the lower (70–280 ng) and higher (420–560 ng) amounts. This may be important for effectively precipitating eDNA during protocol testing.
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Bruno A, Sandionigi A, Agostinetto G, Bernabovi L, Frigerio J, Casiraghi M, Labra M. Food Tracking Perspective: DNA Metabarcoding to Identify Plant Composition in Complex and Processed Food Products. Genes (Basel) 2019; 10:genes10030248. [PMID: 30934656 PMCID: PMC6470991 DOI: 10.3390/genes10030248] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022] Open
Abstract
One of the main goals of the quality control evaluation is to identify contaminants in raw material, or contamination after a food is processed and before it is placed on the market. During the treatment processes, contamination, both accidental and economically motivated, can generate incongruence between declared and real composition. In our study, we evaluated if DNA metabarcoding is a suitable tool for unveiling the composition of processed food, when it contains small trace amounts. We tested this method on different types of commercial plant products by using tnrL marker and we applied amplicon-based high-throughput sequencing techniques to identify plant components in different food products. Our results showed that DNA metabarcoding can be an effective approach for food traceability in different type of processed food. Indeed, the vast majority of our samples, we identified the species composition as the labels reported. Although some critical issues still exist, mostly deriving from the starting composition (i.e., variable complexity in taxa composition) of the sample itself and the different processing level (i.e., high or low DNA degradation), our data confirmed the potential of the DNA metabarcoding approach also in quantitative analyses for food composition quality control.
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Affiliation(s)
- Antonia Bruno
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
| | - Anna Sandionigi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
| | - Giulia Agostinetto
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
| | - Lorenzo Bernabovi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
| | | | - Maurizio Casiraghi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
| | - Massimo Labra
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
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A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining. Sci Data 2019; 6:190008. [PMID: 30747914 PMCID: PMC6371960 DOI: 10.1038/sdata.2019.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/11/2018] [Indexed: 12/25/2022] Open
Abstract
Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.
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12
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Bruno A, Sandionigi A, Bernasconi M, Panio A, Labra M, Casiraghi M. Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy). Front Microbiol 2018; 9:2557. [PMID: 30429832 PMCID: PMC6220058 DOI: 10.3389/fmicb.2018.02557] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | - Antonella Panio
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Bicocca cEnter of Science and Technology for FOOD, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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13
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Mezzasalma V, Sandionigi A, Guzzetti L, Galimberti A, Grando MS, Tardaguila J, Labra M. Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards. Front Microbiol 2018; 9:946. [PMID: 29867854 PMCID: PMC5962658 DOI: 10.3389/fmicb.2018.00946] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022] Open
Abstract
Recent studies have highlighted the role of the grapevine microbiome in addressing a wide panel of features, ranging from the signature of field origin to wine quality. Although the influence of cultivar and vineyard environmental conditions in shaping the grape microbiome have already been ascertained, several aspects related to this topic, deserve to be further investigated. In this study, we selected three international diffused grapevine cultivars (Cabernet Sauvignon, Syrah, and Sauvignon Blanc) at three germplasm collections characterized by different climatic conditions [Northern Italy (NI), Italian Alps (AI), and Northern Spain (NS)]. The soil and grape microbiome was characterized by 16s rRNA High Throughput Sequencing (HTS), and the obtained results showed that all grape samples shared some bacterial taxa, regardless of sampling locality (e.g., Bacillus, Methylobacterium, Sphingomonas, and other genera belonging to Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria). However, some Operational Taxonomic Units (OTUs) could act as geographical signatures and in some cases as cultivar fingerprint. Concerning the origin of the grape microbiome, our study confirms that vineyard soil represents a primary reservoir for grape associated bacteria with almost 60% of genera shared between the soil and grape. At each locality, grapevine cultivars shared a core of bacterial genera belonging to the vineyard soil, as well as from other local biodiversity elements such as arthropods inhabiting or foraging in the vineyard. Finally, a machine learning analysis showed that it was possible to predict the geographical origin and cultivar of grape starting from its microbiome composition with a high accuracy (9 cases out of 12 tested samples). Overall, these findings open new perspectives for the development of more comprehensive and integrated research activities to test which environmental variables have an effective role in shaping the microbiome composition and dynamics of cultivated species over time and space.
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Affiliation(s)
- Valerio Mezzasalma
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Lorenzo Guzzetti
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Andrea Galimberti
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,BEST4FOOD, University of Milano-Bicocca, Milan, Italy
| | - Maria S Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Javier Tardaguila
- Instituto de Ciencias de la Vid y del Vino, University of La Rioja, CSIC, Rioja Regional Government, Logroño, Spain
| | - Massimo Labra
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,BEST4FOOD, University of Milano-Bicocca, Milan, Italy
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Nardone V, Bosso L, Corte MD, Sasso M, Galimberti A, Bruno A, Casiraghi M, Russo D. Native red foxes depredate nests of alien pond sliders: Evidence from molecular detection of prey in scats. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Mezzasalma V, Sandionigi A, Bruni I, Bruno A, Lovicu G, Casiraghi M, Labra M. Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production. PLoS One 2017; 12:e0184615. [PMID: 28892512 PMCID: PMC5593190 DOI: 10.1371/journal.pone.0184615] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022] Open
Abstract
Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits’ microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.
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Affiliation(s)
- Valerio Mezzasalma
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- FEM2-Ambiente s.r.l., Milan, Italy
| | - Anna Sandionigi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Ilaria Bruni
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Antonia Bruno
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Gianni Lovicu
- Agricultural Research Agency of Sardinia (AGRIS), Sassari-Fertilia, Sassari, Italy
| | - Maurizio Casiraghi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- * E-mail:
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Bruno A, Sandionigi A, Rizzi E, Bernasconi M, Vicario S, Galimberti A, Cocuzza C, Labra M, Casiraghi M. Exploring the under-investigated "microbial dark matter" of drinking water treatment plants. Sci Rep 2017; 7:44350. [PMID: 28290543 PMCID: PMC5349567 DOI: 10.1038/srep44350] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 02/09/2017] [Indexed: 11/09/2022] Open
Abstract
Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term "microbial dark matter" was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water.
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Affiliation(s)
- Antonia Bruno
- University of Milan-Bicocca, ZooPlantLab, Biotechnology and Biosciences Department, Piazza della Scienza 2, 20126, Milan, Italy
| | - Anna Sandionigi
- University of Milan-Bicocca, ZooPlantLab, Biotechnology and Biosciences Department, Piazza della Scienza 2, 20126, Milan, Italy
| | - Ermanno Rizzi
- National Research Council (CNR), Institute of Biomedical Technologies (ITB), Via Fratelli Cervi, 93, 20090 Segrate (MI), Italy.,Fondazione Telethon Piazza Cavour, 1, 20121, Milan, Italy
| | - Marzia Bernasconi
- Metropolitana Milanese S.p.A., Via Giuseppe Meda 44, 20141, Milan, Italy
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research, National ResearchCouncil, C/O Physics Department, University of Bari "Aldo Moro", Via Giovanni Amendola, 173 70126, Bari, Italy.,National Research Council (CNR), Institute of Biomedical and Technologies (ITB), via Giovanni Amendola, 122/D, 70126, Bari, Italy
| | - Andrea Galimberti
- University of Milan-Bicocca, ZooPlantLab, Biotechnology and Biosciences Department, Piazza della Scienza 2, 20126, Milan, Italy
| | - Clementina Cocuzza
- University of Milan-Bicocca, Medicine and Surgery Department, Via Cadore 48, 20126, Monza, Italy
| | - Massimo Labra
- University of Milan-Bicocca, ZooPlantLab, Biotechnology and Biosciences Department, Piazza della Scienza 2, 20126, Milan, Italy
| | - Maurizio Casiraghi
- University of Milan-Bicocca, ZooPlantLab, Biotechnology and Biosciences Department, Piazza della Scienza 2, 20126, Milan, Italy
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17
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Bruno A, Sandionigi A, Galimberti A, Siani E, Labra M, Cocuzza C, Ferri E, Casiraghi M. One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria. Microbiologyopen 2016; 6. [PMID: 27790854 PMCID: PMC5300880 DOI: 10.1002/mbo3.421] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 11/21/2022] Open
Abstract
We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high‐throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high‐throughput‐based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Eleonora Siani
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Clementina Cocuzza
- Medicine and Surgery Department, University of Milano-Bicocca, Monza, Italy
| | - Emanuele Ferri
- FEM2-Ambiente, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
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