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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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2
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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3
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Yancey CE, Smith DJ, Den Uyl PA, Mohamed OG, Yu F, Ruberg SA, Chaffin JD, Goodwin KD, Tripathi A, Sherman DH, Dick GJ. Metagenomic and Metatranscriptomic Insights into Population Diversity of Microcystis Blooms: Spatial and Temporal Dynamics of mcy Genotypes, Including a Partial Operon That Can Be Abundant and Expressed. Appl Environ Microbiol 2022; 88:e0246421. [PMID: 35438519 PMCID: PMC9088275 DOI: 10.1128/aem.02464-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) degrade freshwater ecosystems globally. Microcystis aeruginosa often dominates cyanoHABs and produces microcystin (MC), a class of hepatotoxins that poses threats to human and animal health. Microcystin toxicity is influenced by distinct structural elements across a diversity of related molecules encoded by variant mcy operons. However, the composition and distribution of mcy operon variants in natural blooms remain poorly understood. Here, we characterized the variant composition of mcy genes in western Lake Erie Microcystis blooms from 2014 and 2018. Sampling was conducted across several spatial and temporal scales, including different bloom phases within 2014, extensive spatial coverage on the same day (2018), and frequent, autonomous sampling over a 2-week period (2018). Mapping of metagenomic and metatranscriptomic sequences to reference sequences revealed three Microcystis mcy genotypes: complete (all genes present [mcyA-J]), partial (truncated mcyA, complete mcyBC, and missing mcyD-J), and absent (no mcy genes). We also detected two different variants of mcyB that may influence the production of microcystin congeners. The relative abundance of these genotypes was correlated with pH and nitrate concentrations. Metatranscriptomic analysis revealed that partial operons were, at times, the most abundant genotype and expressed in situ, suggesting the potential biosynthesis of truncated products. Quantification of genetic divergence between genotypes suggests that the observed strains are the result of preexisting heterogeneity rather than de novo mutation during the sampling period. Overall, our results show that natural Microcystis populations contain several cooccurring mcy genotypes that dynamically shift in abundance spatiotemporally via strain succession and likely influence the observed diversity of the produced congeners. IMPORTANCE Cyanobacteria are responsible for producing microcystins (MCs), a class of potent and structurally diverse toxins, in freshwater systems around the world. While microcystins have been studied for over 50 years, the diversity of their chemical forms and how this variation is encoded at the genetic level remain poorly understood, especially within natural populations of cyanobacterial harmful algal blooms (cyanoHABs). Here, we leverage community DNA and RNA sequences to track shifts in mcy genes responsible for producing microcystin, uncovering the relative abundance, expression, and variation of these genes. We studied this phenomenon in western Lake Erie, which suffers annually from cyanoHAB events, with impacts on drinking water, recreation, tourism, and commercial fishing.
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Affiliation(s)
- Colleen E. Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Derek J. Smith
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul A. Den Uyl
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
| | - Osama G. Mohamed
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Fengan Yu
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A. Ruberg
- National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory, Ann Arbor, Michigan, USA
| | - Justin D. Chaffin
- F. T. Stone Laboratory, The Ohio State University, Put-In-Bay, Ohio, USA
- Ohio Sea Grant, The Ohio State University, Put-In-Bay, Ohio, USA
| | - Kelly D. Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory (AOML), NOAA, Miami, Florida, USA
- Southwest Fisheries Science Center, NOAA, La Jolla, California, USA
| | - Ashootosh Tripathi
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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4
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Jibrin MO, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Goss EM, Jones JB. Bacterial Spot of Tomato and Pepper in Africa: Diversity, Emergence of T5 Race, and Management. Front Microbiol 2022; 13:835647. [PMID: 35509307 PMCID: PMC9058171 DOI: 10.3389/fmicb.2022.835647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial spot disease was first reported from South Africa by Ethel M. Doidge in 1920. In the ensuing century after the initial discovery, the pathogen has gained global attention in plant pathology research, providing insights into host-pathogen interactions, pathogen evolution, and effector discovery, such as the first discovery of transcription activation-like effectors, among many others. Four distinct genetic groups, including Xanthomonas euvesicatoria (proposed name: X. euvesicatoria pv. euvesicatoria), Xanthomonas perforans (proposed name: X. euvesicatoria pv. perforans), Xanthomonas gardneri (proposed name: Xanthomonas hortorum pv. gardneri), and Xanthomonas vesicatoria, are known to cause bacterial spot disease. Recently, a new race of a bacterial spot pathogen, race T5, which is a product of recombination between at least two Xanthomonas species, was reported in Nigeria. In this review, our focus is on the progress made on the African continent, vis-à-vis progress made in the global bacterial spot research community to provide a body of information useful for researchers in understanding the diversity, evolutionary changes, and management of the disease in Africa.
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Affiliation(s)
- Mustafa Ojonuba Jibrin
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Gerald V. Minsavage
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Garry E. Vallad
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Pamela D. Roberts
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- UF/IFAS Southwest Florida Research and Education Center, Immokalee, FL, United States
| | - Erica M. Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
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5
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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6
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Shi J, Sun Y, Wang X, Wang J. Microplastics reduce soil microbial network complexity and ecological deterministic selection. Environ Microbiol 2022; 24:2157-2169. [PMID: 35229440 DOI: 10.1111/1462-2920.15955] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Abstract
Microplastics have been proposed as emerging threats for terrestrial systems as they may potentially alter the physicochemical/biophysical soil environments. Due to the variety of properties of microplastics and soils, the microplastic-induced effects in soil ecosystems are greatly manifold. Here, we studied effects of three polymer microplastics (polyamide-6 (PA), polyethylene (PE), and polyethylene terephthalate (PET)) on soil properties with four different soil types. The success patterns, interaction relationships, and assembly processes of soil bacterial communities were also studied. Microplastics have the potential to promote CO2 emissions and enhance soil humification. Even though microplastics did not significantly alter the diversity and composition of the soil microbial community, the application of microplastics decreased the network complexity and stability, including network size, connectivity, and the number of module and keystone species. The bacterial community assembly was governed by deterministic selection (77.3% - 90.9%) in all treatments, while microplastics increased the contribution of stochastic processes from 9.1% in control to 13.6% - 22.7%. The neutral model results also indicated most of the bacterial taxa were present in the predicted neutral region (approximately 98%), suggesting the importance of stochastic processes. These findings provided a fundamental insight in understanding the effects of microplastics on soil ecosystems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jia Shi
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiang Wang
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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7
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Fountain-Jones NM, Smith ML, Austerlitz F. Machine learning in molecular ecology. Mol Ecol Resour 2021; 21:2589-2597. [PMID: 34738721 DOI: 10.1111/1755-0998.13532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Affiliation(s)
| | - Megan L Smith
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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8
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Thiele-Bruhn S. The role of soils in provision of genetic, medicinal and biochemical resources. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200183. [PMID: 34365823 PMCID: PMC8349636 DOI: 10.1098/rstb.2020.0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
Intact, 'healthy' soils provide indispensable ecosystem services that largely depend on the biotic activity. Soil health is connected with human health, yet, knowledge of the underlying soil functioning remains incomplete. This review highlights selected services, i.e. (i) soil as a genetic resource and hotspot of biodiversity, forming the basis for providing (ii) biochemical resources and (iii) medicinal services and goods. Soils harbour an unrivalled biodiversity of organisms, especially microorganisms. Some of the abilities of autochthonous microorganisms and their relevant enzymes serve (i) to improve natural soil functions and in particular plant growth, e.g. through beneficial plant growth-promoting, symbiotic and mycorrhizal microorganisms, (ii) to act as biopesticides, (iii) to facilitate biodegradation of pollutants for soil bioremediation and (iv) to yield enzymes or chemicals for industrial use. Soils also exert direct effects on human health. Contact with soil enriches the human microbiome, affords protection against allergies and promotes emotional well-being. Medicinally relevant are soil substrates such as loams, clays and various minerals with curative effects as well as pharmaceutically active organic chemicals like antibiotics that are formed by soil microorganisms. By contrast, irritating minerals, soil dust inhalation and misguided soil ingestion may adversely affect humans. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People.
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Affiliation(s)
- Sören Thiele-Bruhn
- Soil Science, University of Trier, Behringstrasse 21, D-54286 Trier, Germany
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9
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Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol 2021; 22:178. [PMID: 34120611 PMCID: PMC8201837 DOI: 10.1186/s13059-021-02393-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/27/2021] [Indexed: 01/15/2023] Open
Abstract
Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered "high-quality" metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.
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Affiliation(s)
- Askarbek Orakov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Supriya Khedkar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel R Mende
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, 03722, South Korea.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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10
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He Q, Wang S, Hou W, Feng K, Li F, Hai W, Zhang Y, Sun Y, Deng Y. Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145465. [PMID: 33571767 DOI: 10.1016/j.scitotenv.2021.145465] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China.
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Wanming Hai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yuxuan Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
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11
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Nichols RG, Davenport ER. The relationship between the gut microbiome and host gene expression: a review. Hum Genet 2021; 140:747-760. [PMID: 33221945 PMCID: PMC7680557 DOI: 10.1007/s00439-020-02237-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
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Affiliation(s)
- Robert G. Nichols
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Emily R. Davenport
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
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12
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Li W, Li X. Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings. ENVIRONMENTAL MICROBIOME 2021; 16:9. [PMID: 33926573 PMCID: PMC8086273 DOI: 10.1186/s40793-021-00380-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/17/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants' survival. RESULTS In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. CONCLUSIONS Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.
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Affiliation(s)
- Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Key Laboratory for Agricultural Water Resource, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Key Laboratory for Agricultural Water Resource, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China.
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13
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Choe YH, Kim M, Lee YK. Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert. Front Microbiol 2021; 11:607396. [PMID: 33488547 PMCID: PMC7819959 DOI: 10.3389/fmicb.2020.607396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.
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Affiliation(s)
- Yong-Hoe Choe
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
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14
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Albanese D, Donati C. Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. Methods Mol Biol 2021; 2242:153-172. [PMID: 33961223 DOI: 10.1007/978-1-0716-1099-2_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recovering and annotating bacterial genomes from metagenomes involves a series of complex computational tools that are often difficult to use for researches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.
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Affiliation(s)
- Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
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15
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Hu W, Pan J, Wang B, Guo J, Li M, Xu M. Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales). Environ Microbiol 2020; 23:3695-3709. [PMID: 33295091 DOI: 10.1111/1462-2920.15349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023]
Abstract
Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.
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Affiliation(s)
- Wenzhe Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jie Pan
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Li
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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16
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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17
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Soil Microbial Community Profiling and Bacterial Metabolic Activity of Technosols as an Effect of Soil Properties following Land Reclamation: A Case Study from the Abandoned Iron Sulphide and Uranium Mine in Rudki (South-Central Poland). AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10111795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.
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18
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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19
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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20
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David L, Vicedomini R, Richard H, Carbone A. Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinformatics 2020; 36:3975-3981. [PMID: 32330240 PMCID: PMC7332565 DOI: 10.1093/bioinformatics/btaa272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/11/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Motivation The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly ‘explore’ the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly. Results S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains—a typical scenario—S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size. Availability and implementation S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Laurent David
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238
| | - Riccardo Vicedomini
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238.,Sorbonne Université, CNRS, Institut des Sciences du Calcul et des Données (ISCD)
| | - Hugues Richard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238.,Bioinformatics Unit (MF1), Robert Koch Institute, Berlin 13353, Germany
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238.,Institut Universitaire de France, Paris 75005, France
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21
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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 2020; 86:AEM.00140-20. [PMID: 32169939 DOI: 10.1128/aem.00140-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022] Open
Abstract
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.
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22
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Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems 2020; 5:5/1/e00795-19. [PMID: 31911466 PMCID: PMC6946796 DOI: 10.1128/msystems.00795-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.
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Wang W, Su Y, Wang B, Wang Y, Zhuang L, Zhu G. Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:629-640. [PMID: 31170597 DOI: 10.1016/j.scitotenv.2019.04.415] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.
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Affiliation(s)
- Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Baoling Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
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Prabha R, Singh DP. Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders. 3 Biotech 2019; 9:87. [PMID: 30800598 DOI: 10.1007/s13205-019-1635-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Phylogenetic studies based on a definite set of marker genes usually reconstruct evolutionary relationships among the prokaryotic species. Based on specific target sequences, such studies represent variations and allow identification of similarities or dissimilarities in organisms. With the advent of completely sequenced genomes and accumulation of information on whole prokaryotic genomes, phylogenetic reconstructions should be considered more reliable if they are ideally based on entire genomes to resolve phylogenetic interest. We applied phylogenomics approaches taking into account completely sequenced cyanobacterial genomes to reconstruct underlying species that represented major taxonomic classes and belonged to distinctly different habitats (freshwater, marine, soils, and rocks). We did not rely on describing phylogeny of all representative class of cyanobacterial species on the basis of only ribosomal gene, 16S rDNA gene. In contrast, we analyzed combined molecular marker and phylogenomics approaches (genome alignment, gene content and gene order, composition vector and protein domain content) for accurately inferring phylogenetic relationship of species. We have shown that this approach reflects the impact of evolution on the organisms and considers connects with the ecological adaptation in cyanobacteria in different habitats. Analysis revealed that the members from marine habitat occupy different profile than those from freshwater. Impact of GC content and genomic repetitiveness over the diversification of cyanobacterial species and their possible role in adaptation was also reflected. Members occupying similar habitats cover more evolutionary distance together and also evolve various strategies for adaptation and survival either through genomic repetitiveness or preferences for genes of particular functions or modified GC content. Genomes undergo different changes for their adaptation in diverse habitats.
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Affiliation(s)
- Ratna Prabha
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, 275101 India
- 2Department of Biotechnology, Mewar University, Gangrar, Chittorgarh, Rajasthan India
| | - Dhananjaya P Singh
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, 275101 India
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Yu K, Yi S, Li B, Guo F, Peng X, Wang Z, Wu Y, Alvarez-Cohen L, Zhang T. An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community. MICROBIOME 2019; 7:16. [PMID: 30728080 PMCID: PMC6366072 DOI: 10.1186/s40168-019-0634-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/25/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. RESULTS The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. CONCLUSION The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.
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Affiliation(s)
- Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA.
- Environmental microbiology and bioinformatics Laboratory, Shenzhen Graduate School, Peking University, Nanshan district, Shenzhen, Guangdong, China.
| | - Shan Yi
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
| | - Bing Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Feng Guo
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xingxing Peng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhiping Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Wu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
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Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, Hallsworth JE. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. FEMS Microbiol Rev 2018; 42:672-693. [PMID: 29893835 DOI: 10.1093/femsre/fuy026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/08/2018] [Indexed: 11/12/2022] Open
Abstract
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.
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Affiliation(s)
- Callum J D Lee
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Callum J O'Kane
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Rocco L Mancinelli
- BAER Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA
| | - Geoffrey McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de Valencia (CSIC-UV), Valencia, 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 9190401, Israel
| | - Mike L Dyall-Smith
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
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Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Dev Res 2018; 80:86-97. [PMID: 30370682 DOI: 10.1002/ddr.21466] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.
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Affiliation(s)
- Teresa Nogueira
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro H C David
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Muséum National d'Histoire naturelle, CNRS, EPHE, CP, Paris, France
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28
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Ugarte A, Vicedomini R, Bernardes J, Carbone A. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. MICROBIOME 2018; 6:149. [PMID: 30153857 PMCID: PMC6114274 DOI: 10.1186/s40168-018-0532-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/13/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples. RESULTS MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples. CONCLUSIONS Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.
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Affiliation(s)
- Ari Ugarte
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
| | - Riccardo Vicedomini
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
- Sorbonne Université, UPMC-Univ P6, CNRS, Institut des Sciences du Calcul et des Donnees, 4 Place Jussieu, Paris, 75005 France
| | - Juliana Bernardes
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
| | - Alessandra Carbone
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
- Institut Universitaire de France, Paris, 75005 France
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29
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P. De Leon M, Montecillo AD, Pinili DS, Siringan MAT, Park DS. Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano. PLoS One 2018; 13:e0200095. [PMID: 30024917 PMCID: PMC6053158 DOI: 10.1371/journal.pone.0200095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Bats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. The bacterial diversity of two bat guano samples, C1 and C2, from Cabalyorisa Cave, Mabini, Pangasinan, Philippines were investigated using 16S rRNA gene amplicon sequencing. V3-V4 hypervariable regions were amplified and then sequenced using Illumina MiSeq 250 PE system. Reads were processed using Mothur and QIIME pipelines and assigned 12,345 OTUs for C1 and 5,408 OTUs for C2. The most dominant OTUs in C1 belong to the Proteobacteria (61.7%), Actinobacteria (19.4%), Bacteroidetes (4.2%), Firmicutes (2.7%), Chloroflexi (2.5%), candidate phylum TM7 (2.3%) and Planctomycetes (1.9%) while Proteobacteria (61.7%) and Actinobacteria (34.9%) dominated C2. Large proportion of sequence reads mainly associated with unclassified bacteria indicated possible occurrence of novel bacteria in both samples. XRF spectrophotometric analyses of C1 and C2 guano revealed significant differences in the composition of both major and trace elements. C1 guano recorded high levels of Si, Fe, Mg, Al, Mn, Ti and Cu while C2 samples registered high concentrations of Ca, P, S, Zn and Cr. Community structure of the samples were compared with other published community profiling studies from Finland (SRR868695), Meghalaya, Northeast India (SRR1793374) and Maharashtra State, India (CGS). Core microbiome among samples were determined for comparison. Variations were observed among previously studied guano samples and the Cabalyorisa Cave samples were attributed to either bat sources or age of the guano. This is the first study on bacterial diversity of guano in the Philippines through high-throughput sequencing.
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Affiliation(s)
- Marian P. De Leon
- Microbial Culture Collection, Museum of Natural History, University of the Philippines Los Baños, College, Laguna, Philippines
- * E-mail:
| | - Andrew D. Montecillo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Dale S. Pinili
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Maria Auxilia T. Siringan
- Microbiological Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Doo-Sang Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
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30
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Cheaib B, Le Boulch M, Mercier PL, Derome N. Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient. Front Microbiol 2018; 9:869. [PMID: 29774016 PMCID: PMC5943556 DOI: 10.3389/fmicb.2018.00869] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 04/16/2018] [Indexed: 11/29/2022] Open
Abstract
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Malo Le Boulch
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.,GenPhySE, Institut National de la Recherche Agronomique, Université de Toulouse, INPT, ENVT, Castanet-Tolosan, France
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
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31
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Morales‐Cruz A, Allenbeck G, Figueroa‐Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D. Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. MOLECULAR PLANT PATHOLOGY 2018; 19:490-503. [PMID: 28218463 PMCID: PMC6638111 DOI: 10.1111/mpp.12544] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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Affiliation(s)
- Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Gabrielle Allenbeck
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Vanessa E. Ashworth
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Renaud Travadon
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Rhonda J. Smith
- University of California Cooperative Extension, Sonoma CountySanta RosaCA95403USA
| | - Kendra Baumgartner
- United States Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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32
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Swenson TL, Karaoz U, Swenson JM, Bowen BP, Northen TR. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nat Commun 2018; 9:19. [PMID: 29296020 PMCID: PMC5750228 DOI: 10.1038/s41467-017-02356-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 11/21/2017] [Indexed: 11/15/2022] Open
Abstract
Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust. Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).
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Affiliation(s)
- Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Ulas Karaoz
- Climate and Ecosystems Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Joel M Swenson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.,DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA. .,DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA.
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34
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Lopes SP, Azevedo NF, Pereira MO. Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress. Int J Med Microbiol 2017; 307:460-470. [PMID: 29033313 DOI: 10.1016/j.ijmm.2017.09.018] [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: 05/26/2017] [Revised: 08/30/2017] [Accepted: 09/28/2017] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure. Low fluctuations in biofilm compositions were observed across distinct oxygen environments, with dual-species biofilms exhibiting similar relative proportions and P. aeruginosa and/or D. pigrum populations dominating three-species consortia. Once exposed to antibiotics, biofilms displayed high resistance profiles, and microbial compositions, distributions, and microbial interactions significantly challenged. The antibiotic/oxygen environment supported such fluctuations, which enhanced for three-species communities. In conclusion, antibiotic therapy hugely disturbed CF communities' dynamics, inducing significant compositional changes on multispecies consortia. Clearly, multiple perturbations may disturb this dynamic, giving rise to various microbiological scenarios in vivo, and affecting disease phenotype. Therefore, an appreciation of the ecological/evolutionary nature within CF communities will be useful for the optimal use of current therapies and for newer breakthroughs on CF antibiotherapy.
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Affiliation(s)
- Susana Patrícia Lopes
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Nuno Filipe Azevedo
- LEPABE - Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Maria Olívia Pereira
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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35
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Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725-731. [PMID: 28787424 PMCID: PMC6436528 DOI: 10.1038/nbt.3893] [Citation(s) in RCA: 1123] [Impact Index Per Article: 160.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/27/2017] [Indexed: 12/20/2022]
Abstract
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed. We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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Affiliation(s)
- Robert M Bowers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Devin Doud
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Jessica Jarett
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Adam R Rivers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,United States Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Gainesville, Florida, USA
| | | | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oakridge Tennessee, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - George M Garrity
- Department of Microbiology &Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, California, USA
| | - Shibu Yooseph
- J. Craig Venter Institute, San Diego, California, USA
| | | | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - William C Nelson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven J Hallam
- Department of Microbiology &Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,Center for Dark Energy Biosphere Investigation, University of Southern California, Los Angeles, California, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Scott Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, Burlington Vermont, USA
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Austin, Texas, USA
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Brian Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Rob Knight
- Center for Microbiome Innovation, and Departments of Pediatrics and Computer Science &Engineering, University of California San Diego, La Jolla, California, USA
| | - Rob Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Alla Lapidus
- Centre for Algorithmic Biotechnology, ITBM, St. Petersburg State University, St. Petersburg, Russia
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - A M Eren
- Knapp Center for Biomedical Discovery, Chicago, Illinois, USA
| | - Lynn Schriml
- National Cancer Institute, Frederick, Maryland, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
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Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment. Appl Environ Microbiol 2017; 83:AEM.00729-17. [PMID: 28667104 PMCID: PMC5561297 DOI: 10.1128/aem.00729-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/20/2017] [Indexed: 02/06/2023] Open
Abstract
During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.
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Microbial competition in porous environments can select against rapid biofilm growth. Proc Natl Acad Sci U S A 2016; 114:E161-E170. [PMID: 28007984 DOI: 10.1073/pnas.1525228113] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow-biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.
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38
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Ribière C, Beugnot R, Parisot N, Gasc C, Defois C, Denonfoux J, Boucher D, Peyretaillade E, Peyret P. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning. Methods Mol Biol 2016; 1399:167-82. [PMID: 26791503 DOI: 10.1007/978-1-4939-3369-3_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
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Affiliation(s)
- Céline Ribière
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Réjane Beugnot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Nicolas Parisot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Cyrielle Gasc
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Clémence Defois
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Jérémie Denonfoux
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
- Genoscreen, Campus de l'Institut Pasteur de Lille, 59000, Lille, France.
| | - Delphine Boucher
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Eric Peyretaillade
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
| | - Pierre Peyret
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
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39
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Shah B, Jain K, Jiyani H, Mohan V, Madamwar D. Microaerophilic Symmetric Reductive Cleavage of Reactive Azo Dye—Remazole Brilliant Violet 5R by Consortium VIE6: Community Synergism. Appl Biochem Biotechnol 2016; 180:1029-1042. [DOI: 10.1007/s12010-016-2150-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
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40
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Poelchau MF, Coates BS, Childers CP, Peréz de León AA, Evans JD, Hackett K, Shoemaker D. Agricultural applications of insect ecological genomics. CURRENT OPINION IN INSECT SCIENCE 2016; 13:61-69. [PMID: 27436554 DOI: 10.1016/j.cois.2015.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 12/07/2015] [Accepted: 12/13/2015] [Indexed: 06/06/2023]
Abstract
Agricultural entomology is poised to benefit from the application of ecological genomics, particularly the fields of biofuels generation and pest control. Metagenomic methods can characterize microbial communities of termites, wood-boring beetles and livestock pests, and transcriptomic approaches reveal molecular bases behind wood-digesting capabilities of these insects, leading to potential mechanisms for biofuel generation. Genome sequences are being exploited to develop new pest control methods, identify candidate antigens to vaccinate livestock, and discover RNAi target sequences and potential non-target effects in other insects. Gene content analyses of pest genome sequences and their endosymbionts suggest metabolic interdependencies between organisms, exposing potential gene targets for insect control. Finally, genome-wide association studies and genotyping by high-throughput sequencing promise to improve management of pesticide resistance.
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Affiliation(s)
- Monica F Poelchau
- USDA-ARS, National Agricultural Library, Beltsville, MD 20705, United States.
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, United States
| | | | - Adalberto A Peréz de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX 78028, United States
| | - Jay D Evans
- USDA-ARS, Bee Research Laboratory, Beltsville, MD 20705, United States
| | - Kevin Hackett
- USDA-ARS, Office of National Programs, Crop Production and Protection, Beltsville, MD 20705, United States
| | - DeWayne Shoemaker
- USDA-ARS, Imported Fire Ant and Household Insects Research Unit, Gainesville, FL 32608, United States.
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41
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Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME JOURNAL 2015; 10:858-70. [PMID: 26394009 DOI: 10.1038/ismej.2015.162] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/21/2015] [Accepted: 07/31/2015] [Indexed: 02/05/2023]
Abstract
Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.
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Abstract
Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been "in culture" for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the "parts list" (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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44
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White RL, Sutton AE, Salguero-Gómez R, Bray TC, Campbell H, Cieraad E, Geekiyanage N, Gherardi L, Hughes AC, Jørgensen PS, Poisot T, DeSoto L, Zimmerman N. The next generation ofaction ecology: novel approaches towards global ecological research. Ecosphere 2015. [DOI: 10.1890/es14-00485.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Fahy A, Giloteaux L, Bertin P, Le Paslier D, Médigue C, Weissenbach J, Duran R, Lauga B. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage. MICROBIAL ECOLOGY 2015; 70:154-167. [PMID: 25592635 DOI: 10.1007/s00248-014-0558-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
To gain an in-depth insight into the diversity and the distribution of genes under the particular evolutionary pressure of an arsenic-rich acid mine drainage (AMD), the genes involved in bacterial arsenic detoxification (arsB, ACR3) and arsenite oxidation (aioA) were investigated in sediment from Carnoulès (France), in parallel to the diversity and global distribution of the metabolically active bacteria. The metabolically active bacteria were affiliated mainly to AMD specialists, i.e., organisms detected in or isolated from AMDs throughout the world. They included mainly Acidobacteria and the non-affiliated "Candidatus Fodinabacter communificans," as well as Thiomonas and Acidithiobacillus spp., Actinobacteria, and unclassified Gammaproteobacteria. The distribution range of these organisms suggested that they show niche conservatism. Sixteen types of deduced protein sequences of arsenite transporters (5 ArsB and 11 Acr3p) were detected, whereas a single type of arsenite oxidase (AioA) was found. Our data suggested that at Carnoulès, the aioA gene was more recent than those encoding arsenite transporters and subjected to a different molecular evolution. In contrast to the 16S ribosomal RNA (16S rRNA) genes associated with AMD environments worldwide, the functional genes aioA, ACR3, and to a lesser extent arsB, were either novel or specific to Carnoulès, raising the question as to whether these functional genes are specific to high concentrations of arsenic, AMD-specific, or site-specific.
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Affiliation(s)
- Anne Fahy
- Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
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46
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Gasc C, Ribière C, Parisot N, Beugnot R, Defois C, Petit-Biderre C, Boucher D, Peyretaillade E, Peyret P. Capturing prokaryotic dark matter genomes. Res Microbiol 2015; 166:814-30. [PMID: 26100932 DOI: 10.1016/j.resmic.2015.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022]
Abstract
Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
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Affiliation(s)
- Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Céline Ribière
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Nicolas Parisot
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France.
| | - Réjane Beugnot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Clémence Defois
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Corinne Petit-Biderre
- Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171 Aubière, France.
| | - Delphine Boucher
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Eric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
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47
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Nnadozie CF, Lin J, Govinden R. Selective isolation of bacteria for metagenomic analysis: Impact of membrane characteristics on bacterial filterability. Biotechnol Prog 2015; 31:853-66. [DOI: 10.1002/btpr.2109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/20/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Chika F. Nnadozie
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
| | - Johnson Lin
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
| | - Roshini Govinden
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
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48
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Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME JOURNAL 2015; 9:2697-711. [PMID: 25918833 DOI: 10.1038/ismej.2015.66] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects.
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Affiliation(s)
- Katherine McMahon
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin, Madison, WI, USA
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