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Kazmi SSUH, Tayyab M, Pastorino P, Barcelò D, Yaseen ZM, Grossart HP, Khan ZH, Li G. Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134574. [PMID: 38739959 DOI: 10.1016/j.jhazmat.2024.134574] [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: 02/13/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.
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Affiliation(s)
- Syed Shabi Ul Hassan Kazmi
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Muhammad Tayyab
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 Torino, Italy
| | - Damià Barcelò
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), 08034 Barcelona, Spain
| | - Zaher Mundher Yaseen
- Civil and Environmental Engineering Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, (IGB), Alte Fischerhuette 2, Neuglobsow, D-16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany
| | - Zulqarnain Haider Khan
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
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2
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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3
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Bocci V, Galafassi S, Levantesi C, Crognale S, Amalfitano S, Congestri R, Matturro B, Rossetti S, Di Pippo F. Freshwater plastisphere: a review on biodiversity, risks, and biodegradation potential with implications for the aquatic ecosystem health. Front Microbiol 2024; 15:1395401. [PMID: 38699475 PMCID: PMC11064797 DOI: 10.3389/fmicb.2024.1395401] [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: 03/03/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
The plastisphere, a unique microbial biofilm community colonizing plastic debris and microplastics (MPs) in aquatic environments, has attracted increasing attention owing to its ecological and public health implications. This review consolidates current state of knowledge on freshwater plastisphere, focussing on its biodiversity, community assembly, and interactions with environmental factors. Current biomolecular approaches revealed a variety of prokaryotic and eukaryotic taxa associated with plastic surfaces. Despite their ecological importance, the presence of potentially pathogenic bacteria and mobile genetic elements (i.e., antibiotic resistance genes) raises concerns for ecosystem and human health. However, the extent of these risks and their implications remain unclear. Advanced sequencing technologies are promising for elucidating the functions of plastisphere, particularly in plastic biodegradation processes. Overall, this review emphasizes the need for comprehensive studies to understand plastisphere dynamics in freshwater and to support effective management strategies to mitigate the impact of plastic pollution on freshwater resources.
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Affiliation(s)
- Valerio Bocci
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Silvia Galafassi
- Water Research Institute, CNR-IRSA, National Research Council, Verbania, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Caterina Levantesi
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Simona Crognale
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Stefano Amalfitano
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Roberta Congestri
- Laboratory of Biology of Algae, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Bruna Matturro
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Simona Rossetti
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Francesca Di Pippo
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
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4
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Hechler RM, Yates MC, Chain FJJ, Cristescu ME. Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Mol Ecol 2023. [PMID: 37792902 DOI: 10.1111/mec.17152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
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Affiliation(s)
- Robert M Hechler
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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5
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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6
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Krinos AI, Cohen NR, Follows MJ, Alexander H. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:74. [PMID: 36869298 PMCID: PMC9983209 DOI: 10.1186/s12859-022-05121-y] [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: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
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Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. .,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. .,Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
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Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
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8
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Tonelli A, Lumngwena EN, Ntusi NAB. The oral microbiome in the pathophysiology of cardiovascular disease. Nat Rev Cardiol 2023; 20:386-403. [PMID: 36624275 DOI: 10.1038/s41569-022-00825-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2022] [Indexed: 01/11/2023]
Abstract
Despite advances in our understanding of the pathophysiology of many cardiovascular diseases (CVDs) and expansion of available therapies, the global burden of CVD-associated morbidity and mortality remains unacceptably high. Important gaps remain in our understanding of the mechanisms of CVD and determinants of disease progression. In the past decade, much research has been conducted on the human microbiome and its potential role in modulating CVD. With the advent of high-throughput technologies and multiomics analyses, the complex and dynamic relationship between the microbiota, their 'theatre of activity' and the host is gradually being elucidated. The relationship between the gut microbiome and CVD is well established. Much less is known about the role of disruption (dysbiosis) of the oral microbiome; however, interest in the field is growing, as is the body of literature from basic science and animal and human investigations. In this Review, we examine the link between the oral microbiome and CVD, specifically coronary artery disease, stroke, peripheral artery disease, heart failure, infective endocarditis and rheumatic heart disease. We discuss the various mechanisms by which oral dysbiosis contributes to CVD pathogenesis and potential strategies for prevention and treatment.
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Affiliation(s)
- Andrea Tonelli
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa.,Cardiovascular Research Unit, Christiaan Barnard Division of Cardiothoracic Surgery, Department of Surgery, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa.,Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Extramural Research Unit on the Intersection of Noncommunicable Diseases and Infectious Disease, South African Medical Research Council, Cape Town, South Africa
| | - Evelyn N Lumngwena
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.,Centre for the Study of Emerging and Re-emerging Infections, Institute for Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Ntobeko A B Ntusi
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa. .,Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Extramural Research Unit on the Intersection of Noncommunicable Diseases and Infectious Disease, South African Medical Research Council, Cape Town, South Africa. .,Cape Universities Body Imaging Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Wellcome Centre for Infectious Disease Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [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: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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10
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Koch RA, Herr JR. Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. Front Microbiol 2021; 12:733159. [PMID: 34803949 PMCID: PMC8602889 DOI: 10.3389/fmicb.2021.733159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/14/2021] [Indexed: 01/30/2023] Open
Abstract
Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.
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Affiliation(s)
- Rachel A. Koch
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, United States
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11
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Jia S, Li T, Zhang XX. Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1610-1619. [PMID: 33278015 DOI: 10.1007/s10646-020-02313-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Ultraviolet (UV) disinfection is now widely implemented in wastewater treatment plants (WWTPs) worldwide, but its effect on antibiotic resistome of the surviving bacteria remains unclear. In this study, we employed high-throughput sequencing-based metagenomic and metatranscriptomic approaches to comprehensively elucidate the effects of UV disinfection on the shifts of bacterial community and antibiotic resistance genes (ARGs) on both DNA and mRNA levels in one WWTP. Metagenomic analyses revealed an insignificant change in the bacterial community after UV disinfection, while metatranscriptomic analyses showed that UV disinfection significantly changed the abundance of 13.79% of phyla and 10.32% of genera. In total, 38 ARG-like open reading frames (ORFs) and 327 ARG-like transcripts were identified in the DNA and RNA samples, respectively. The relative abundances of the total ARGs, each ARG type, and each ARG subtype also varied after UV disinfection. Additionally, UV disinfection significantly reduced the expression of total ARGs from 49.40 transcripts per kilobase of exon model per million mapped reads (TPM) to 47.62 TPM, and significantly changed the expression of 10.75% of ARG subtypes in wastewater (p < 0.05). Notably, the significant increase in the expression and obvious increase in the relative abundance of macrolide-lincosamide-streptogramin B (MLSB) resistance genes revealed that UV disinfection increases the potential health risk of MLSB resistance genes in wastewater. Moreover, potential host analyses of ARGs revealed the different preferences of antibiotic resistant bacteria (ARB) to ARGs. This study may shed new light on the underlying mechanism of the UV disinfection effect on antibiotic resistance.
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Affiliation(s)
- Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Tong Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China.
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12
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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13
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Fukuba T, Fujii T. Lab-on-a-chip technology for in situ combined observations in oceanography. LAB ON A CHIP 2021; 21:55-74. [PMID: 33300537 DOI: 10.1039/d0lc00871k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The oceans sustain the global environment and diverse ecosystems through a variety of biogeochemical processes and their complex interactions. In order to understand the dynamism of the local or global marine environments, multimodal combined observations must be carried out in situ. On the other hand, instrumentation of in situ measurement techniques enabling biological and/or biochemical combined observations is challenging in aquatic environments, including the ocean, because biochemical flow analyses require a more complex configuration than physicochemical electrode sensors. Despite this technical hurdle, in situ analyzers have been developed to measure the concentrations of seawater contents such as nutrients, trace metals, and biological components. These technologies have been used for cutting-edge ocean observations to elucidate the biogeochemical properties of water mass with a high spatiotemporal resolution. In this context, the contribution of lab-on-a-chip (LoC) technology toward the miniaturization and functional integration of in situ analyzers has been gaining momentum. Due to their mountability, in situ LoC technologies provide ideal instrumentation for underwater analyzers, especially for miniaturized underwater observation platforms. Consequently, the appropriate combination of reliable LoC and underwater technologies is essential to realize practical in situ LoC analyzers suitable for underwater environments, including the deep sea. Moreover, the development of fundamental LoC technologies for underwater analyzers, which operate stably in extreme environments, should also contribute to in situ measurements for public or industrial purposes in harsh environments as well as the exploration of the extraterrestrial frontier.
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Affiliation(s)
- Tatsuhiro Fukuba
- Institute for Marine-Earth Exploration and Engineering, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho 2-15, Yokosuka, Kanagawa 237-0061, Japan.
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14
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Inomura K, Deutsch C, Masuda T, Prášil O, Follows MJ. Quantitative models of nitrogen-fixing organisms. Comput Struct Biotechnol J 2020; 18:3905-3924. [PMID: 33335688 PMCID: PMC7733014 DOI: 10.1016/j.csbj.2020.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 10/26/2022] Open
Abstract
Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiol 2020; 92:103606. [PMID: 32950142 DOI: 10.1016/j.fm.2020.103606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023]
Abstract
Table olives are considered the most widespread fermented food in the Mediterranean area and their consumption is expanding all over the world. This fermented vegetable can be considered as a natural functional food thanks to their high nutritional value and high content of bioactive compounds that contribute to the health and well-being of consumers. The presence of bioactive compounds is strongly influenced by a complex microbial consortium, traditionally exploited through culture-dependent approaches. Recently, the rapid spread of omics technologies has represented an important challenge to better understand the function, the adaptation and the exploitation of microbial diversity in different complex ecosystems, such as table olives. This review provides an overview of the potentiality of omics technologies to in depth investigate the microbial composition and the metabolic processes that drive the table olives fermentation, affecting both sensorial profile and safety properties of the final product. Finally, the review points out the role of omics approaches to raise at higher sophisticated level the investigations on microbial, gene, protein, and metabolite, with huge potential for the integration of table olives composition with functional assessments.
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16
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Xu T, Gong Y, Su X, Zhu P, Dai J, Xu J, Ma B. Phenome-Genome Profiling of Single Bacterial Cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001172. [PMID: 32519499 DOI: 10.1002/smll.202001172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/01/2020] [Indexed: 06/11/2023]
Abstract
The small size and low DNA amount of bacterial cells have hindered establishing phenome-genome links in a precisely indexed, one-cell-per-reaction manner. Here, Raman-Activated Gravity-driven single-cell Encapsulation and Sequencing (RAGE-Seq) is presented, where individual cells are phenotypically screened via single-cell Raman spectra (SCRS) in an aquatic, vitality-preserving environment, then the cell with targeted SCRS is precisely packaged in a picoliter microdroplet and readily exported in a precisely indexed, "one-cell-one-tube" manner. Such integration of microdroplet encapsulation to Raman-activated sorting ensures high-coverage one-cell genome sequencing or cultivation that is directly linked to metabolic phenotype. For clinical Escherichia coli isolates, genome assemblies derived from precisely one cell via RAGE-Seq consistently reach >95% coverage. Moreover, directly from a urine sample of urogenital tract infection, metabolic-activity-based antimicrobial susceptibility phenotypes and genome sequence of 99.5% coverage are obtained simultaneously from precisely one cell. This single-cell global mutation map corroborates resistance phenotype and genotype, and unveils epidemiological features with high specificity and sensitivity. The ability to profile and correlate bacterial metabolic phenome and high-quality genome sequences at one-cell resolution suggests broad application of RAGE-Seq.
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Affiliation(s)
- Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Xiaolu Su
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Pengfei Zhu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Jing Dai
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
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17
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Shoemaker KM, McCliment EA, Moisander PH. Copepod-Associated Gammaproteobacterial Alkaline Phosphatases in the North Atlantic Subtropical Gyre. Front Microbiol 2020; 11:1033. [PMID: 32523576 PMCID: PMC7261903 DOI: 10.3389/fmicb.2020.01033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Abstract
Planktonic organisms may provide a niche to associated bacteria in the oligotrophic ocean. Bacterial fitness strategies in association with copepods - abundant planktonic crustaceans - were examined by sampling and incubation experiments in the North Atlantic Subtropical Gyre (NASG). The bacterial metatranscriptome was dominated by Gammaproteobacteria and showed expression of complete bacterial pathways including chemotaxis, cell signaling, and alkaline phosphatase activity. Quantitative PCR and reverse transcriptase qPCR revealed the consistent presence and expression of alkaline phosphatase genes primarily by Vibrio spp. in the copepod association. Copepod-associated bacteria appear to respond to prevailing phosphorus limitation by using alkaline phosphatases to break down organophosphoesters, presumably originating from the copepods. The results suggest that the basin-wide tendency for phosphorus limitation in the North Atlantic Ocean is occurring at microscales in these nitrogen-enriched copepod microenvironments. The bacterial communities and their fitness strategies supported by associations with these abundant mesozooplankton are unique from the surrounding seawater and could have large-scale implications for biogeochemical cycling, marine food web structuring, and copepod and ecosystem health.
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Affiliation(s)
- Katyanne M Shoemaker
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Elizabeth A McCliment
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Pia H Moisander
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
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18
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Palma E, Tilocca B, Roncada P. Antimicrobial Resistance in Veterinary Medicine: An Overview. Int J Mol Sci 2020; 21:E1914. [PMID: 32168903 PMCID: PMC7139321 DOI: 10.3390/ijms21061914] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
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Affiliation(s)
| | | | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (E.P.); (B.T.)
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19
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Heravi FS, Zakrzewski M, Vickery K, Hu H. Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. J Microbiol Methods 2020; 170:105856. [DOI: 10.1016/j.mimet.2020.105856] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/13/2023]
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20
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Bozcal E, Dagdeviren M. Bacterial metagenome analysis of Mytilus galloprovincialis collected from Istanbul and Izmir coastal stations of Turkey. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:186. [PMID: 32072329 DOI: 10.1007/s10661-020-8129-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Mytilus galloprovincialis is a marine mollusk belonging to the Bivalvia class. It has been distributed largely in Turkish shores and worldwide aquatic environments. Besides being known as an environmental pollution indicator, it is highly consumed as a food and has a high economic value. Due to their nutritional mechanisms by filtering water, they are affected by pollution in seawater and mussels can host-microbial diversity of environmental origin as well as pathogenic bacteria. Therefore, in this study, bacterial species found in Mediterranean mussels collected from the coastal stations of Istanbul [Rumeli Kavagi (RK), Kucukcekmece (KC)], and Izmir [(Foca (MF), Urla (MU)] were investigated and compared with microbiological and metagenomic analyses. According to microbiological analysis results, 34 mussel-associated Enterobacteriaceae and Vibrionaceae family members were identified. As a result of the culture-independent metagenomic analysis, taxonomic groups for each station were identified and compared based on Operational Taxonomic Unit data. For all stations, the most abundant bacterial genera were the unclassified bacterial genera. The total number of mussel-related total richness identified in all groups was 4889 (RK = 1605; KC = 1930; MF = 1508; and MU = 1125). According to the metagenomic data obtained in this study, different relative amounts of Lachnospiraceae and Bacteroidetes taxa groups were reported for all stations. The pathogenic bacterial genera identified by metagenomic analyses which may be significant for the public health are Arcobacter, Clostridium, Aeromonas, Vibrio, Escherichia_Shigella, Klebsiella, Campylobacter, Helicobacter, Pseudomonas, Morganella, Serratia, Corynebacterium, Enterococcus, Staphylococcus, Yersinia, Mycoplasma, Brucellaceae_unclassified, Pantoea, and Proteus.
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Affiliation(s)
- Elif Bozcal
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
| | - Melih Dagdeviren
- Department of Biology, Faculty of Science, Ege University, Bornova, 35040, Izmir, Turkey
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21
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Brumfield KD, Huq A, Colwell RR, Olds JL, Leddy MB. Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data. PLoS One 2020; 15:e0228899. [PMID: 32053657 PMCID: PMC7018008 DOI: 10.1371/journal.pone.0228899] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/24/2020] [Indexed: 01/01/2023] Open
Abstract
Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.
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Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - James L. Olds
- Schar School, George Mason University, Arlington, Virginia, United States of America
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, California, United States of America
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22
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Sharma PK, Sharma V, Sharma S, Bhatia G, Singh K, Sharma R. Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil. J Genet Eng Biotechnol 2019; 17:6. [PMID: 31659568 PMCID: PMC6821142 DOI: 10.1186/s43141-019-0006-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Studying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil). RESULTS Analysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides. CONCLUSION Altogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.
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Affiliation(s)
| | - Vinay Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Miyapur, Hyderabad, Telangana 500 049 India
| | - Garima Bhatia
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Rohit Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
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23
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Shakya M, Lo CC, Chain PSG. Advances and Challenges in Metatranscriptomic Analysis. Front Genet 2019; 10:904. [PMID: 31608125 PMCID: PMC6774269 DOI: 10.3389/fgene.2019.00904] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/26/2019] [Indexed: 11/13/2022] Open
Abstract
Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.
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Affiliation(s)
- Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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24
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Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom. Appl Environ Microbiol 2019; 85:AEM.00349-19. [PMID: 31126952 DOI: 10.1128/aem.00349-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/25/2019] [Indexed: 02/02/2023] Open
Abstract
Given the ecological significance of microorganisms in algal blooming events, it is critical to understand the mechanisms regarding their distribution under different conditions. We tested the hypothesis that microbial community succession is strongly associated with algal bloom stages, and that the assembly mechanisms are cocontrolled by deterministic and stochastic processes. Community structures and underlying ecological processes of microbial populations (attached and free-living bacteria) at three algal bloom stages (pre-, during, and postbloom) over a complete dinoflagellate Scrippsiella trochoidea bloom were investigated. Both attached and free-living taxa had a strong response to the bloom event, and the latter was more sensitive than the former. The contribution of environmental parameters to microbial variability was 40.2%. Interaction analysis showed that complex positive or negative correlation networks exist in phycosphere microbes. These relationships were the potential drivers of mutualist and competitive interactions that impacted bacterial succession. Null model analysis showed that the attached bacterial community primarily exhibited deterministic processes at pre- and during-bloom stages, while dispersal-related processes contributed to a greater extent at the postbloom stage. In the free-living bacterial community, homogeneous selection and dispersal limitation dominated in the initial phase, which gave way to more deterministic processes at the two later stages. Relative contribution analyses further demonstrated that the community turnover of attached bacteria was mainly driven by environmental selection, while stochastic factors had partial effects on the assembly of free-living bacteria. Taken together, these data demonstrated that a robust link exists between bacterioplankton community structure and bloom progression, and phycosphere microbial succession trajectories are cogoverned by both deterministic and random processes.IMPORTANCE Disentangling the mechanisms shaping bacterioplankton communities during a marine ecological event is a core concern for ecologists. Harmful algal bloom (HAB) is a typical ecological disaster, and its formation is significantly influenced by alga-bacterium interactions. Microbial community shifts during the HAB process are relatively well known. However, the assembly processes of microbial communities in an HAB are not fully understood, especially the relative influences of deterministic and stochastic processes. We therefore analyzed the relative contributions of deterministic and stochastic processes during an HAB event. Both free-living and attached bacterial groups had a dramatic response to the HAB, and the relative importance of determinism versus stochasticity varied between the two bacterial groups at various bloom stages. Environmental factors and biotic interactions were the main drivers impacting the microbial shift process. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns during the HAB process.
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Miro-Blanch J, Yanes O. Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism. Front Genet 2019; 10:638. [PMID: 31338107 PMCID: PMC6628876 DOI: 10.3389/fgene.2019.00638] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023] Open
Abstract
Gut microbiota communities have coevolved for millions of years in a symbiotic relationship with their mammalian hosts. Elucidating and understanding the molecular mechanisms by which microbiota interacts with its host and how this contributes to the homeostasis of the host is crucial. One of these molecular relationships is the so-called chemical crosstalk between microbiota and host metabolisms, including the poorly explored epigenetic regulation of host tissues by the metabolic activity of gut microbiota in response to changes in diet. DNA methylation and histone modifications are epigenetic marks partly regulated by enzymes such as methylases and acetylases, whose activity depend on host and microbiota metabolites that act as substrates and cofactors for these reactions. However, providing a complete mechanistic description of the regulatory interactions between both metabolisms and the impact on the expression of host genes through an epigenetic modulation, remains elusive. This article presents our perspective on how metabolomic, metagenomic, transcriptomic, and epigenomic data can be used to investigate the "microbiota-nutrient metabolism-epigenetics axis." We also discuss the implications and opportunities this knowledge may have for basic and applied science, such as the impact on the way we structure future research, understand, and prevent diseases like type 2 diabetes or obesity.
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Affiliation(s)
- Joan Miro-Blanch
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Oscar Yanes
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Agyirifo DS, Wamalwa M, Otwe EP, Galyuon I, Runo S, Takrama J, Ngeranwa J. Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. Heliyon 2019; 5:e02170. [PMID: 31388591 PMCID: PMC6667825 DOI: 10.1016/j.heliyon.2019.e02170] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/05/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.
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Affiliation(s)
- Daniel S. Agyirifo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Mark Wamalwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- International Livestock Research Institute-Bioscience East and Central Africa, Kenya
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Isaac Galyuon
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Steven Runo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
| | - Jemmy Takrama
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
- Cocoa Research Institute of Ghana, Ghana
| | - Joseph Ngeranwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
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Thorn CE, Bergesch C, Joyce A, Sambrano G, McDonnell K, Brennan F, Heyer R, Benndorf D, Abram F. A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures. Mol Ecol Resour 2019; 19:439-455. [PMID: 30565880 DOI: 10.1111/1755-0998.12979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022]
Abstract
The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.
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Affiliation(s)
- Camilla E Thorn
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christian Bergesch
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aoife Joyce
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Gustavo Sambrano
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Kevin McDonnell
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Fiona Brennan
- Department of Environment, Soils and Land-use, Teagasc, Wexford, Ireland
| | - Robert Heyer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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Amato P, Besaury L, Joly M, Penaud B, Deguillaume L, Delort AM. Metatranscriptomic exploration of microbial functioning in clouds. Sci Rep 2019; 9:4383. [PMID: 30867542 PMCID: PMC6416334 DOI: 10.1038/s41598-019-41032-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.
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Affiliation(s)
- Pierre Amato
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France.
| | - Ludovic Besaury
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Muriel Joly
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Benjamin Penaud
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | | | - Anne-Marie Delort
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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Yang H, Wang J, Lv Z, Tian J, Peng Y, Peng X, Xu X, Song Q, Lv B, Chen Z, Sun Z, Wang Z. Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 159:1-9. [PMID: 29730401 DOI: 10.1016/j.ecoenv.2018.04.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Cadmium (Cd) generates a variety of physiological and ecological toxicity to spiders. However, little is known about the effects of Cd on symbiotic bacteria of spiders. Metatranscriptomics is increasing our knowledge of microorganisms in environment. To better understand the impact of Cd on the symbiotic bacteria of spiders, we generated and compared the metatranscriptomes of the intestinal microorganisms of Pardosa pseudoannulata with and without Cd stress. The community structure of intestinal microorganisms in P. pseudoannulata was composed of 4 kingdoms, namely bacteria, viruses, eukaryotes and archaea, including 46 phyla, 97 classes, 184 orders, 339 families, 470 genera, and 598 species. The abundance of eukaryotes, bacteria and viruses was decreased by 0.14%, 1.22% and 2.52% respectively while the archaea was increased by 99.16% when under Cd stress. We identified 1519 differentially expressed genes (DEGs), including 770 up-regulated and 749 down-regulated genes. The results of KEGG annotation revealed that the expression of genes that are involved in the carbon metabolism, protein and amino acid metabolism and synthesis, glucose metabolism, oxidative phosphorylation, and glutathione metabolism were influenced by Cd. Collectively, these findings showed that Cd significantly impacted the community structure and expression of related functional genes of intestinal microorganisms in P. pseudoannulata.
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Affiliation(s)
- Huilin Yang
- College of Orient Science & Technology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China; College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Juan Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhiyue Lv
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jianxiang Tian
- College of Continuing Education, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China.
| | - Xianjin Peng
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
| | - Xiang Xu
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Bo Lv
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhaoyang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhiying Sun
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhi Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China; College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
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Rotimi AM, Pierneef R, Reva ON. Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools. BMC Bioinformatics 2018; 19:309. [PMID: 30165813 PMCID: PMC6117900 DOI: 10.1186/s12859-018-2320-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/21/2018] [Indexed: 11/23/2022] Open
Abstract
Background Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level. Results In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za/. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect. Conclusions The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za/) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.
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Affiliation(s)
- Adeola M Rotimi
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria, 0002, South Africa
| | - Rian Pierneef
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria, 0002, South Africa.,Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria, 0002, South Africa.
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Albright MBN, Johansen R, Lopez D, Gallegos-Graves LV, Steven B, Kuske CR, Dunbar J. Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil. Appl Environ Microbiol 2018; 84:e00598-18. [PMID: 29802185 PMCID: PMC6052259 DOI: 10.1128/aem.00598-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/15/2018] [Indexed: 01/05/2023] Open
Abstract
Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.
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Affiliation(s)
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Blaire Steven
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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Palazzotto E, Weber T. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol 2018; 45:109-116. [PMID: 29656009 DOI: 10.1016/j.mib.2018.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics.
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Affiliation(s)
- Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark.
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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Gandhi A, Shah NP. Integrating omics to unravel the stress-response mechanisms in probiotic bacteria: Approaches, challenges, and prospects. Crit Rev Food Sci Nutr 2018; 57:3464-3471. [PMID: 26853094 DOI: 10.1080/10408398.2015.1136805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Identifying the stress-response mechanism of probiotic bacteria has always captivated the interest of food producers. It is crucial to identify probiotic bacteria that have increased stress tolerance to survive during production, processing, and storage of food products. However, in order to achieve high resistance to environmental factors, there is a need to better understand stress-induced responses and adaptive mechanisms. With advances in bacterial genomics, there has been an upsurge in the application of other omic platforms such as transcriptomics, proteomics, metabolomics, and some more recent ones such as interactomics, fluxomics, and phenomics. These omic technologies have revolutionized the functional genomics and their application. There have been several studies implementing various omic technologies to investigate the stress responses of probiotic bacteria. Integrated omics has the potential to provide in-depth information about the mechanisms of stress-induced responses in bacteria. However, there remain challenges in integrating information from different omic platforms. This review discusses current omic techniques and challenges faced in integrating various omic platforms with focus on their use in stress-response studies.
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Affiliation(s)
- Akanksha Gandhi
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
| | - Nagendra P Shah
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
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Pinatel E, Peano C. RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction. Methods Mol Biol 2018; 1716:239-265. [PMID: 29222757 DOI: 10.1007/978-1-4939-7528-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is a strict interplay between metabolic networks and transcriptional regulation in bacteria; indeed, the transcriptome regulation, affecting the expression of large gene sets, can be used to predict the likely "on" or "off" state of metabolic genes as a function of environmental factors. Up to date, many bacterial transcriptomes have been studied by RNAseq, hundreds of experiments have been performed, and Giga bases of sequences have been produced. All this transcriptional information could potentially be integrated into metabolic networks in order to obtain a more comprehensive view of their regulation and to increase their prediction power.To get high-quality transcriptomic data, to be integrated into metabolic networks, it is paramount to clearly know how to produce highly informative RNA sequencing libraries and how to manage RNA sequencing data.In this chapter, we will get across the main steps of an RNAseq experiment: from removal of ribosomal RNAs, to strand-specific library preparation, till data analysis and integration. We will try to share our experience and know-how, to give you a precise protocol to follow, and some useful recommendations or tips and tricks to adopt in order to go straightforward toward a successful RNAseq experiment.
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Affiliation(s)
- Eva Pinatel
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Milan, Italy.
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Crovadore J, Soljan V, Calmin G, Chablais R, Cochard B, Lefort F. Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents. Heliyon 2017; 3:e00427. [PMID: 29062974 PMCID: PMC5647474 DOI: 10.1016/j.heliyon.2017.e00427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/06/2017] [Accepted: 10/11/2017] [Indexed: 11/18/2022] Open
Abstract
Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.
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Affiliation(s)
- Julien Crovadore
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - Vice Soljan
- Puratis Sàrl, EPFL Innovation Park, Building C, 1015 Lausanne, Switzerland
| | - Gautier Calmin
- Faculty of Engineering and Architecture, HES-SO University of Applied Sciences and Arts Western Switzerland, Rue de la Jeunesse 1, 2800 Delémont, Switzerland
| | - Romain Chablais
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - Bastien Cochard
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - François Lefort
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
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Klingenberg H, Meinicke P. How to normalize metatranscriptomic count data for differential expression analysis. PeerJ 2017; 5:e3859. [PMID: 29062598 PMCID: PMC5649605 DOI: 10.7717/peerj.3859] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/06/2017] [Indexed: 11/25/2022] Open
Abstract
Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ widely. Our studies indicate that in real data applications performed with global scaling it might be impossible to distinguish between differential expression in terms of transcriptomic changes and differential composition in terms of changing taxonomic proportions. Conclusions As in transcriptomics, a proper normalization of count data is also essential for differential expression analysis in metatranscriptomics. Our model implies a taxon-specific scaling of counts for normalization of the data. The application of taxon-specific scaling consequently removes taxonomic composition variations from functional profiles and therefore provides a clear interpretation of the observed functional differences.
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Affiliation(s)
- Heiner Klingenberg
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
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40
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Yan YW, Zou B, Zhu T, Hozzein WN, Quan ZX. Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. PLoS One 2017; 12:e0186161. [PMID: 29016661 PMCID: PMC5634646 DOI: 10.1371/journal.pone.0186161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/26/2017] [Indexed: 11/19/2022] Open
Abstract
RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.
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Affiliation(s)
- Yong-Wei Yan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Wael N. Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- * E-mail:
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41
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Zinke LA, Mullis MM, Bird JT, Marshall IPG, Jørgensen BB, Lloyd KG, Amend JP, Kiel Reese B. Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:528-536. [PMID: 28836742 DOI: 10.1111/1758-2229.12578] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.
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Affiliation(s)
- Laura A Zinke
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
| | - Megan M Mullis
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
| | - Jordan T Bird
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, USA
| | | | | | - Karen G Lloyd
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, USA
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Galia W, Leriche F, Cruveiller S, Garnier C, Navratil V, Dubost A, Blanquet-Diot S, Thevenot-Sergentet D. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. BMC Genomics 2017; 18:574. [PMID: 28774270 PMCID: PMC5543532 DOI: 10.1186/s12864-017-3957-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. RESULTS Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. CONCLUSION In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.
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Affiliation(s)
- Wessam Galia
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France.
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France.
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France.
| | - Francoise Leriche
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute Genoscope & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, Evry, France
| | - Cindy Garnier
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Audrey Dubost
- UMR 5557 Ecologie Microbienne, CNRS, Université de Lyon, Lyon, France
| | - Stéphanie Blanquet-Diot
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Thevenot-Sergentet
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
- Reference Laboratory for Escherichia coli including Shiga Toxin-Producing E. coli, VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, Marcy l'Etoile, Lyon, France
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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Zhu YG, Xue XM, Kappler A, Rosen BP, Meharg AA. Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7326-7339. [PMID: 28602082 PMCID: PMC5871744 DOI: 10.1021/acs.est.7b00689] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.
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Affiliation(s)
- Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xi-Mei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Andrew A Meharg
- Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5HN, United Kingdom
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An Alternative Method to Niskin Sampling for Molecular Analysis of the Marine Environment. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2017. [DOI: 10.3390/jmse5020022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Towards a sustainable biobased industry - Highlighting the impact of extremophiles. N Biotechnol 2017; 40:144-153. [PMID: 28512003 DOI: 10.1016/j.nbt.2017.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/28/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022]
Abstract
The transition of the oil-based economy towards a sustainable economy completely relying on biomass as renewable feedstock requires the concerted action of academia, industry, politics and civil society. An interdisciplinary approach of various fields such as microbiology, molecular biology, chemistry, genetics, chemical engineering and agriculture in addition to cross-sectional technologies such as economy, logistics and digitalization is necessary to meet the future global challenges. The genomic era has contributed significantly to the exploitation of naturés biodiversity also from extreme habitats. By applying modern technologies it is now feasible to deliver robust enzymes (extremozymes) and robust microbial systems that are active at temperatures up to 120°C, at pH 0 and 12 and at 1000bar. In the post-genomic era, different sophisticated "omics" analyses will allow the identification of countless novel enzymes regardless of the lack of cultivability of most microorganisms. Furthermore, elaborate protein-engineering methods are clearing the way towards tailor-made robust biocatalysts. Applying environmentally friendly and efficient biological processes, terrestrial and marine biomass can be converted to high value products e.g. chemicals, building blocks, biomaterials, pharmaceuticals, food, feed and biofuels. Thus, further application of extremophiles has the potential to improve sustainability of existing biotechnological processes towards a greener biobased industry.
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Effects of Gelling Agent and Extracellular Signaling Molecules on the Culturability of Marine Bacteria. Appl Environ Microbiol 2017; 83:AEM.00243-17. [PMID: 28213548 DOI: 10.1128/aem.00243-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/15/2017] [Indexed: 01/08/2023] Open
Abstract
Only 1% of marine bacteria are currently culturable using standard laboratory procedures, and this is a major obstacle for our understanding of the biology of marine microorganisms and for the discovery of novel microbial natural products. Therefore, the purpose of this study was to investigate if improved cultivation conditions, including the use of an alternative gelling agent and supplementation with signaling molecules, improve the culturability of bacteria from seawater. Replacing agar with gellan gum improved viable counts 3- to 40-fold, depending on medium composition and incubation conditions, with a maximum of 6.6% culturability relative to direct cell counts. Through V4 amplicon sequencing we found that culturable diversity was also affected by a change in gelling agent, facilitating the growth of orders not culturable on agar-based substrates. Community analyses showed that communities grown on gellan gum substrates were significantly different from communities grown on agar and that they covered a larger fraction of the seawater community. Other factors, such as incubation temperature and time, had less obvious effects on viable counts and culturable diversity. Supplementation with acylated homoserine lactones (AHLs) did not have a positive effect on total viable counts or a strong effect on culturable diversity. However, low concentrations of AHLs increased the relative abundance of sphingobacteria. Hence, with alternative growth substrates, it is possible to significantly increase the number and diversity of cultured marine bacteria.IMPORTANCE Serious challenges to human health, such as the occurrence and spread of antibiotic resistance and an aging human population in need of bioactive pharmaceuticals, have revitalized the search for natural microbial products. The marine environment, representing the largest ecosystem in the biosphere, harbors an immense and virtually untapped microbial diversity producing unique bioactive compounds. However, we are currently able to cultivate only a minute fraction of this diversity. The lack of cultivated microbes is hampering not only bioprospecting efforts but also our general understanding of marine microbes. In this study, we present a means to increase the number and diversity of cultured bacteria from seawater, showing that relatively simple changes to medium components may facilitate the isolation and growth of hitherto unknown bacterial orders.
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Hinsu AT, Parmar NR, Nathani NM, Pandit RJ, Patel AB, Patel AK, Joshi CG. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis). Anaerobe 2017; 44:106-116. [PMID: 28246035 DOI: 10.1016/j.anaerobe.2017.02.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 02/18/2017] [Accepted: 02/23/2017] [Indexed: 10/20/2022]
Abstract
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Nidhi R Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Neelam M Nathani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Anand B Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
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Won NI, Kim KH, Kang JH, Park SR, Lee HJ. Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14020130. [PMID: 28134828 PMCID: PMC5334684 DOI: 10.3390/ijerph14020130] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/10/2017] [Indexed: 01/11/2023]
Abstract
The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.
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Affiliation(s)
- Nam-Il Won
- Water Institute, Korea Water Resources Corporation, Daejeon 34350, Korea.
| | | | - Ji Hyoun Kang
- Korean Entomological Institute, Korea University, Seoul 02841, Korea.
| | - Sang Rul Park
- Estuarine and Coastal Ecology Laboratory, Department of Marine Life Sciences, Jeju National University, Jeju 63243, Korea.
| | - Hyuk Je Lee
- Molecular Ecology and Evolution Laboratory, Department of Biological Science, Sangji University, Wonju 26339, Korea.
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