1
|
Maisnam P, Jeffries TC, Szejgis J, Bristol D, Singh BK, Eldridge DJ, Horn S, Chieppa J, Nielsen UN. Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands. Microb Ecol 2023; 86:3097-3110. [PMID: 37878053 PMCID: PMC10640424 DOI: 10.1007/s00248-023-02303-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023]
Abstract
Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.
Collapse
Affiliation(s)
- Premchand Maisnam
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Thomas C Jeffries
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Jerzy Szejgis
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Dylan Bristol
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sebastian Horn
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Jeff Chieppa
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| |
Collapse
|
2
|
Schupfer E, Ooi SL, Jeffries TC, Wang S, Micalos PS, Pak SC. Changes in the Human Gut Microbiome during Dietary Supplementation with Modified Rice Bran Arabinoxylan Compound. Molecules 2023; 28:5400. [PMID: 37513272 PMCID: PMC10385627 DOI: 10.3390/molecules28145400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
This study investigated the effects of a modified rice bran arabinoxylan compound (RBAC) as a dietary supplement on the gut microbiota of healthy adults. Ten volunteers supplemented their diet with 1 g of RBAC for six weeks and 3 g of RBAC for another six weeks, with a three-week washout period. Faecal samples were collected every 3 weeks over 21 weeks. Microbiota from faecal samples were profiled using 16S rRNA sequencing. Assessment of alpha and beta microbiota diversity was performed using the QIIME2 platform. The results revealed that alpha and beta diversity were not associated with the experimental phase, interventional period, RBAC dosage, or time. However, the statistical significance of the participant was detected in alpha (p < 0.002) and beta (weighted unifrac, p = 0.001) diversity. Explanatory factors, including diet and lifestyle, were significantly associated with alpha (p < 0.05) and beta (p < 0.01) diversity. The individual beta diversity of six participants significantly changed (p < 0.05) during the interventional period. Seven participants showed statistically significant taxonomic changes (ANCOM W ≥ 5). These results classified four participants as responders to RBAC supplementation, with a further two participants as likely responders. In conclusion, the gut microbiome is highly individualised and modulated by RBAC as a dietary supplement, dependent on lifestyle and dietary intake.
Collapse
Affiliation(s)
- Emily Schupfer
- School of Dentistry and Medical Sciences, Charles Sturt University, Bathurst, NSW 2795, Australia
| | - Soo Liang Ooi
- School of Dentistry and Medical Sciences, Charles Sturt University, Bathurst, NSW 2795, Australia
| | - Thomas C Jeffries
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Shaoyu Wang
- School of Dentistry and Medical Sciences, Charles Sturt University, Orange, NSW 2800, Australia
- Ageing Well Research Group, Charles Sturt University, Orange, NSW 2800, Australia
| | - Peter S Micalos
- School of Dentistry and Medical Sciences, Charles Sturt University, Port Macquarie, NSW 2444, Australia
| | - Sok Cheon Pak
- School of Dentistry and Medical Sciences, Charles Sturt University, Bathurst, NSW 2795, Australia
| |
Collapse
|
3
|
Jayaramaiah RH, Egidi E, Macdonald CA, Wang J, Jeffries TC, Megharaj M, Singh BK. Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation. Microb Biotechnol 2022; 15:318-336. [PMID: 34689422 PMCID: PMC8719800 DOI: 10.1111/1751-7915.13946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics-contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.
Collapse
Affiliation(s)
- Ramesha H. Jayaramaiah
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
| | - Catriona A. Macdonald
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Jun‐Tao Wang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
| | - Thomas C. Jeffries
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental RemediationThe University of NewcastleCallaghanNSW2308Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
| |
Collapse
|
4
|
O'Carroll DM, Jeffries TC, Lee MJ, Le ST, Yeung A, Wallace S, Battye N, Patch DJ, Manefield MJ, Weber KP. Developing a roadmap to determine per- and polyfluoroalkyl substances-microbial population interactions. Sci Total Environ 2020; 712:135994. [PMID: 31931194 DOI: 10.1016/j.scitotenv.2019.135994] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
We collected over 40 groundwater samples from a per- and polyfluoroalkyl substances (PFAS) impacted legacy fire fighting training area in Canada to develop an in-depth assessment of the relationship between PFAS and in situ microbial communities. Results suggest differential transport of PFAS of differing chain-length and head group. There is also evidence of PFAS degradation, in particular 6:2 FTS degradation. Although PFAS constituents were not major drivers of microbial community structure, the relative abundance of over one hundred individual genera were significantly associated with PFAS chemistry. For example, lineages within the Oxalobacteraceae family had strong negative correlations with PFAS, whilst the Desulfococcus genus has strong positive correlations. Results also suggest a range of genera may have been stimulated at low to mid-range concentrations (e.g., Gordonia and Acidimicrobium), with some genera potentially inhibited at high PFAS concentrations. Any correlations identified need to be further investigated to determine the underlying reasons for observed associations as this is an open field site with the potential for many confounding factors. Positive correlations may ultimately provide important insights related to development of biodegradation technologies for PFAS impacted sites, while negative correlations further improve our understanding of the potential negative effects of PFAS on ecosystem health.
Collapse
Affiliation(s)
- Denis M O'Carroll
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia.
| | | | - Matthew J Lee
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Song Thao Le
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna Yeung
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarah Wallace
- Environmental Sciences Group, Royal Military College of Canada, Kingston, ON, Canada
| | - Nick Battye
- Environmental Sciences Group, Royal Military College of Canada, Kingston, ON, Canada
| | - David J Patch
- Environmental Sciences Group, Royal Military College of Canada, Kingston, ON, Canada
| | - Michael J Manefield
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kela P Weber
- Environmental Sciences Group, Royal Military College of Canada, Kingston, ON, Canada
| |
Collapse
|
5
|
Trevathan-Tackett SM, Jeffries TC, Macreadie PI, Manojlovic B, Ralph P. Long-term decomposition captures key steps in microbial breakdown of seagrass litter. Sci Total Environ 2020; 705:135806. [PMID: 31838420 DOI: 10.1016/j.scitotenv.2019.135806] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Seagrass biomass represents an important source of organic carbon that can contribute to long-term sediment carbon stocks in coastal ecosystems. There is little empirical data on the long-term microbial decomposition of seagrass detritus, despite this process being one of the key drivers of carbon-cycling in coastal ecosystems, that is, it influences the amount and quality of carbon available for sequestration. Here, our goal was to investigate how litter quality (leaf vs. rhizome/root) and the microbial communities involved in organic matter remineralisation shift over a 2-year field decomposition study north of Sydney, Australia using the temperate seagrass Zostera muelleri. The sites varied in bulk sediment characteristics and the sediment-associated microbial communities, but these variables overall had little influence on long-term seagrass decomposition rates or seagrass-associated microbiomes. The results showed a clear succession of bacterial and archaeal communities for both tissues types from r-strategists such as α- and γ-proteobacteria to K-strategies, including δ-proteobacteria, Bacteroidia and Spirochaetes. We used a new mathematical model to capture how decay rates varied over time and found that two decomposition events occurred for some seagrass leaf samples, possibly due to exudate input from living seagrass roots growing into the litter bag. The new model also indicated that conventional single exponential models overestimate long-term decay rates, and we detected for the first time the refractory, or stable, phase of decomposition for rhizome/root biomass. The stable phase began at approximately 20% mass remaining and after 600 days, and the persistence of rhizome/root biomass was attributed to the anoxic conditions and the preservation of refractory organic matter. While we predict that rhizome/root biomass will contribute more to the long-term sediment carbon stocks, the preservation of leaf carbon may be enhanced at locations were sedimentation is high and burial in anoxic conditions is rapid and constant.
Collapse
Affiliation(s)
- Stacey M Trevathan-Tackett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Burwood Campus, VIC 3125, Australia.
| | - Thomas C Jeffries
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2751, Australia
| | - Peter I Macreadie
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Burwood Campus, VIC 3125, Australia
| | - Bojana Manojlovic
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|
6
|
Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
Collapse
Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
| |
Collapse
|
7
|
Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
Collapse
Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
| |
Collapse
|
8
|
Brice KL, Trivedi P, Jeffries TC, Blyton MDJ, Mitchell C, Singh BK, Moore BD. The Koala ( Phascolarctos cinereus) faecal microbiome differs with diet in a wild population. PeerJ 2019; 7:e6534. [PMID: 30972242 PMCID: PMC6448554 DOI: 10.7717/peerj.6534] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022] Open
Abstract
Background The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet. Method The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species Eucalyptus viminalis, the other comprising the less preferred and less digestible species Eucalyptus obliqua. Results Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating E. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the E. viminalis diet produced communities dominated by the genera Parabacteroides and/or Bacteroides, whereas the E. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae. Discussion We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identified Parabacteroides and Ruminococcaceae genomes.
Collapse
Affiliation(s)
- Kylie L Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Bioagricultural Sciences & Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Bioagricultural Sciences & Pest Management, Colorado State University, Fort Collins, CO, United States of America.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Christopher Mitchell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| |
Collapse
|
9
|
Tang FHM, Jeffries TC, Vervoort RW, Conoley C, Coleman NV, Maggi F. Microcosm experiments and kinetic modeling of glyphosate biodegradation in soils and sediments. Sci Total Environ 2019; 658:105-115. [PMID: 30572210 DOI: 10.1016/j.scitotenv.2018.12.179] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Glyphosate (GLP) is one of the most widely-used herbicides globally and its toxicity to humans and the environment is controversial. GLP is biodegradable, but little is known about the importance of site exposure history and other environmental variables on the rate and pathway of biodegradation. Here, GLP was added to microcosms of soils and sediments with different exposure histories and these were incubated with amendments of glucose, ammonium, and phosphate. GLP concentrations were measured with a newly-developed HPLC method capable of tolerating high concentrations of ammonium and amino acids. GLP biodegradation occurred after a lag-time proportional to the level of GLP pre-exposure in anthropogenically-impacted samples (soils and sediments), while no degradation occurred in samples from a pristine sediment after 180 days of incubation. Exposure history did not influence the rate of GLP degradation, after the lag-time was elapsed. Addition of C, N, and P triggered GLP degradation in pristine sediment and shortened the lag-time before degradation in other samples. In all microcosms, GLP was metabolised into aminomethylphosphonic acid (AMPA), which was highly persistent, and thus appears to be a more problematic pollutant than GLP. Bacterial communities changed along the gradients of anthropogenic impacts, but in some cases, taxonomically very-similar communities showed dramatically different activities with GLP. Our findings reveal important interactions between agriculturally-relevant nutrients and herbicides.
Collapse
Affiliation(s)
- Fiona H M Tang
- Laboratory for Advanced Environmental Engineering Research, School of Civil Engineering, The University of Sydney, Bld. J05, 2006 Sydney, NSW, Australia.
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, 2751 Penrith, NSW, Australia
| | - R Willem Vervoort
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Chris Conoley
- Environmental Earth Sciences International Pty Ltd, 82-84 Dickson Ave, Artarmon, NSW, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Federico Maggi
- Laboratory for Advanced Environmental Engineering Research, School of Civil Engineering, The University of Sydney, Bld. J05, 2006 Sydney, NSW, Australia
| |
Collapse
|
10
|
Varkey D, Mazard S, Jeffries TC, Hughes DJ, Seymour J, Paulsen IT, Ostrowski M. Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary. PLoS One 2018; 13:e0209857. [PMID: 30586428 PMCID: PMC6306231 DOI: 10.1371/journal.pone.0209857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/12/2018] [Indexed: 01/14/2023] Open
Abstract
Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap in the phytoplankton community structure and substantial changes associated with transient environmental perturbations, an essential step towards unravelling the dynamics of primary production in a highly urbanised estuarine ecosystem in response to climate change and other anthropogenic stressors.
Collapse
Affiliation(s)
- Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (IP); (DV)
| | - Sophie Mazard
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Thomas C. Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - David J. Hughes
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW, Australia
| | - Justin Seymour
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (IP); (DV)
| | - Martin Ostrowski
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
11
|
Delgado-Baquerizo M, Maestre FT, Eldridge DJ, Bowker MA, Jeffries TC, Singh BK. Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents. New Phytol 2018; 220:824-835. [PMID: 29607501 DOI: 10.1111/nph.15120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/16/2018] [Indexed: 05/23/2023]
Abstract
Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands.
Collapse
Affiliation(s)
- Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 S. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| |
Collapse
|
12
|
Li J, Lin J, Pei C, Lai K, Jeffries TC, Tang G. Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation. PeerJ 2018; 6:e5648. [PMID: 30280026 PMCID: PMC6160830 DOI: 10.7717/peerj.5648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/25/2018] [Indexed: 12/30/2022] Open
Abstract
Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.
Collapse
Affiliation(s)
- Jiayu Li
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, China.,School of Science and Health, University of Western Sydney, Penrith, NSW, Australia
| | - Jiayi Lin
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, China
| | - Chenyu Pei
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, China
| | - Kaitao Lai
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, Australia
| | - Thomas C Jeffries
- School of Science and Health, University of Western Sydney, Penrith, NSW, Australia
| | - Guangda Tang
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, China
| |
Collapse
|
13
|
Jeffries TC, Rayu S, Nielsen UN, Lai K, Ijaz A, Nazaries L, Singh BK. Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils. Front Microbiol 2018. [PMID: 29515526 PMCID: PMC5826299 DOI: 10.3389/fmicb.2018.00147] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.
Collapse
Affiliation(s)
- Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Smriti Rayu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Kaitao Lai
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, Australia
| | - Ali Ijaz
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Loic Nazaries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| |
Collapse
|
14
|
Trevathan-Tackett SM, Seymour JR, Nielsen DA, Macreadie PI, Jeffries TC, Sanderman J, Baldock J, Howes JM, Steven ADL, Ralph PJ. Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions. FEMS Microbiol Ecol 2017; 93:3071444. [PMID: 28334391 DOI: 10.1093/femsec/fix033] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/12/2017] [Indexed: 11/14/2022] Open
Abstract
Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.
Collapse
Affiliation(s)
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Daniel A Nielsen
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Peter I Macreadie
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia.,School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC 3125, Australia
| | - Thomas C Jeffries
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia.,Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2750, Australia
| | - Jonathan Sanderman
- CSIRO Agriculture and Food, Glen Osmond, SA 5064, Australia.,Woods Hole Research Center, Falmouth, MA 02540, USA
| | - Jeff Baldock
- CSIRO Agriculture and Food, Glen Osmond, SA 5064, Australia
| | - Johanna M Howes
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | | | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| |
Collapse
|
15
|
Ijaz AZ, Jeffries TC, Ijaz UZ, Hamonts K, Singh BK. Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences. PeerJ 2017; 5:e3827. [PMID: 29038749 PMCID: PMC5639872 DOI: 10.7717/peerj.3827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/29/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.
Collapse
Affiliation(s)
- Ali Z. Ijaz
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| | - Thomas C. Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
- School of Science & Health, Western Sydney University, Penrith, Australia
- Indigo V Expeditions, Sentosa Cove, Singapore
| | - Umer Z. Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| |
Collapse
|
16
|
Drigo B, Nielsen UN, Jeffries TC, Curlevski NJA, Singh BK, Duursma RA, Anderson IC. Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities. Environ Microbiol 2017; 19:3175-3185. [PMID: 28557350 DOI: 10.1111/1462-2920.13802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 11/27/2022]
Abstract
Global change models indicate that rainfall patterns are likely to shift towards more extreme events concurrent with increasing atmospheric carbon dioxide concentration ([CO2 ]). Both changes in [CO2 ] and rainfall regime are known to impact above- and belowground communities, but the interactive effects of these global change drivers have not been well explored, particularly belowground. In this experimental study, we examined the effects of elevated [CO2 ] (ambient + 240 ppm; [eCO2 ]) and changes in rainfall patterns (seasonal drought) on soil microbial communities associated with forest ecosystems. Our results show that bacterial and archaeal communities are highly resistant to seasonal drought under ambient [CO2 ]. However, substantial taxa specific responses to seasonal drought were observed at [eCO2 ], suggesting that [eCO2 ] compromise the resistance of microbial communities to extreme events. Within the microbial community we were able to identify three types of taxa specific responses to drought: tolerance, resilience and sensitivity that contributed to this pattern. All taxa were tolerant to seasonal drought at [aCO2 ], whereas resilience and sensitivity to seasonal drought were much greater in [eCO2 ]. These results provide strong evidence that [eCO2 ] moderates soil microbial community responses to drought in forests, with potential implications for their long-term persistence and ecosystem functioning.
Collapse
Affiliation(s)
- Barbara Drigo
- University of South Australia, FII, Mawson Lakes, GPO Box 2471, Adelaide, SA, 5001, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Nathalie J A Curlevski
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Remko A Duursma
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| |
Collapse
|
17
|
Delgado‐Baquerizo M, Trivedi P, Trivedi C, Eldridge DJ, Reich PB, Jeffries TC, Singh BK. Microbial richness and composition independently drive soil multifunctionality. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12924] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel Delgado‐Baquerizo
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO USA
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO USA
| | - Chanda Trivedi
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
| | - David J. Eldridge
- School of Biological Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| | - Peter B. Reich
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Department of Forest Resources University of Minnesota St. Paul MN USA
| | - Thomas C. Jeffries
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| |
Collapse
|
18
|
Trivedi P, Delgado‐Baquerizo M, Jeffries TC, Trivedi C, Anderson IC, Lai K, McNee M, Flower K, Pal Singh B, Minkey D, Singh BK. Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content. Environ Microbiol 2017; 19:3070-3086. [DOI: 10.1111/1462-2920.13779] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/20/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort Collins CO80523, USA
| | - Manuel Delgado‐Baquerizo
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Cooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulder CO80309, USA
| | - Thomas C. Jeffries
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Chanda Trivedi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Ian C. Anderson
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Kaitao Lai
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Matthew McNee
- Western Australian No‐Tillage Farmers AssociationLeeuwin Centre, CSIRO65, Brockway RoadFloreat WA6014, Australia
| | - Kenneth Flower
- School of Plant Biology and Institute of AgricultureThe University of Western Australia35 Stirling HighwayCrawley WA6009, Australia
| | - Bhupinder Pal Singh
- NSW Department of Primary IndustriesElizabeth Macarthur Agricultural InstituteMenangle NSW2568, Australia
| | - David Minkey
- Western Australian No‐Tillage Farmers AssociationLeeuwin Centre, CSIRO65, Brockway RoadFloreat WA6014, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Global Centre for Land Based InnovationWestern Sydney UniversityBuilding L9, Locked Bag 1797Penrith South NSW2751, Australia
| |
Collapse
|
19
|
Dann LM, Rosales S, McKerral J, Paterson JS, Smith RJ, Jeffries TC, Oliver RL, Mitchell JG. Marine and giant viruses as indicators of a marine microbial community in a riverine system. Microbiologyopen 2016; 5:1071-1084. [PMID: 27506856 PMCID: PMC5221468 DOI: 10.1002/mbo3.392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.
Collapse
Affiliation(s)
- Lisa M Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Stephanie Rosales
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Jody McKerral
- School of Computer Science, Engineering and Mathematics, Flinders University, Adelaide, Australia
| | - James S Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Renee J Smith
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Rod L Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia
| | - James G Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| |
Collapse
|
20
|
Delgado‐Baquerizo M, Maestre FT, Reich PB, Trivedi P, Osanai Y, Liu Y, Hamonts K, Jeffries TC, Singh BK. Carbon content and climate variability drive global soil bacterial diversity patterns. ECOL MONOGR 2016. [DOI: 10.1002/ecm.1216] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Manuel Delgado‐Baquerizo
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Fernando T. Maestre
- Área de Biodiversidad y Conservación Departamento de Biología y Geología, Física y Química Inorgánica Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos Calle Tulipán Sin Número 28933 Móstoles Spain
| | - Peter B. Reich
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- Department of Forest Resources University of Minnesota St. Paul Minnesota 55108 USA
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Yui Osanai
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Yu‐Rong Liu
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing 100085 China
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Thomas C. Jeffries
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith 2751 New South Wales Australia
| |
Collapse
|
21
|
Trivedi P, Delgado-Baquerizo M, Trivedi C, Hu H, Anderson IC, Jeffries TC, Zhou J, Singh BK. Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships. ISME J 2016; 10:2593-2604. [PMID: 27168143 DOI: 10.1038/ismej.2016.65] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/31/2022]
Abstract
A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.
Collapse
Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Chanda Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
| |
Collapse
|
22
|
Jeffries TC, Schmitz Fontes ML, Harrison DP, Van-Dongen-Vogels V, Eyre BD, Ralph PJ, Seymour JR. Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. Front Microbiol 2016; 6:1438. [PMID: 26858690 PMCID: PMC4726783 DOI: 10.3389/fmicb.2015.01438] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/02/2015] [Indexed: 02/01/2023] Open
Abstract
The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem.
Collapse
Affiliation(s)
- Thomas C. Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney UniversityPenrith, NSW, Australia
| | - Maria L. Schmitz Fontes
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Daniel P. Harrison
- School of Geosciences, University of Sydney Institute of Marine Science, The University of SydneySydney, NSW, Australia
- Sydney Institute of Marine ScienceMosman, NSW, Australia
| | - Virginie Van-Dongen-Vogels
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Bradley D. Eyre
- Centre for Coastal Management, Southern Cross UniversityLismore, NSW, Australia
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| |
Collapse
|
23
|
Nielsen DA, Pernice M, Schliep M, Sablok G, Jeffries TC, Kühl M, Wangpraseurt D, Ralph PJ, Larkum AWD. Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians. Environ Microbiol 2015; 17:4121-32. [PMID: 26176189 DOI: 10.1111/1462-2920.12983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
The cyanobacterium Prochloron didemni is primarily found in symbiotic relationships with various marine hosts such as ascidians and sponges. Prochloron remains to be successfully cultivated outside of its host, which reflects a lack of knowledge of its unique ecophysiological requirements. We investigated the microenvironment and diversity of Prochloron inhabiting the upper, exposed surface of didemnid ascidians, providing the first insights into this microhabitat. The pH and O2 concentration in this Prochloron biofilm changes dynamically with irradiance, where photosynthetic activity measurements showed low light adaptation (Ek ∼ 80 ± 7 μmol photons m(-2) s(-1)) but high light tolerance. Surface Prochloron cells exhibited a different fine structure to Prochloron cells from cloacal cavities in other ascidians, the principle difference being a central area of many vacuoles dissected by single thylakoids in the surface Prochloron. Cyanobacterial 16S rDNA pyro-sequencing of the biofilm community on four ascidians resulted in 433 operational taxonomic units (OTUs) where on average -85% (65-99%) of all sequence reads, represented by 136 OTUs, were identified as Prochloron via blast search. All of the major Prochloron-OTUs clustered into independent, highly supported phylotypes separate from sequences reported for internal Prochloron, suggesting a hitherto unexplored genetic variability among Prochloron colonizing the outer surface of didemnids.
Collapse
Affiliation(s)
- Daniel A Nielsen
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Mathieu Pernice
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Martin Schliep
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Thomas C Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia.,Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales, 2751, Australia
| | - Michael Kühl
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia.,Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, DK-3000, Denmark
| | - Daniel Wangpraseurt
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Anthony W D Larkum
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| |
Collapse
|
24
|
Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, Stocker R, Ralph PJ, Seymour JR. Chemotaxis by natural populations of coral reef bacteria. ISME J 2015; 9:1764-77. [PMID: 25615440 DOI: 10.1038/ismej.2014.261] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 12/27/2022]
Abstract
Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.
Collapse
Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas C Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Katherina Petrou
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Melissa Garren
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roman Stocker
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
25
|
Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ, Seymour JR. Variability in microbial community composition and function between different niches within a coral reef. Microb Ecol 2014; 67:540-552. [PMID: 24477921 DOI: 10.1007/s00248-013-0362-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/26/2013] [Indexed: 06/03/2023]
Abstract
To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.
Collapse
Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW, Australia,
| | | | | | | | | | | |
Collapse
|
26
|
Roudnew B, Lavery TJ, Seymour JR, Jeffries TC, Mitchell JG. Variability in bacteria and virus-like particle abundances during purging of unconfined aquifers. Ground Water 2014; 52:118-124. [PMID: 23550819 DOI: 10.1111/gwat.12044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Standard methodologies for sampling the physicochemical conditions of groundwater recommend purging a bore for three bore volumes to avoid sampling the stagnant water within a bore and instead gain samples representative of the aquifer. However, there are currently no methodological standards addressing the amount of purging required to gain representative biological samples to assess groundwater bacterial and viral abundances. The objective of this study was to examine how bacterial and viral abundances change during the purging of bore volumes. Six bores infiltrating into unconfined aquifers were pumped for five or six bore volumes each and bacteria and virus-like particles (VLPs) were enumerated from each bore volume using flow cytometry. In examination of the individual bores trends in bacterial abundances were observed to increase, decrease, or remain constant with each purged bore volume. Furthermore, triplicates taken at each bore volume indicated substantial variations in VLP and bacterial abundances that are often larger than the differences between bore volumes. This indicates a high level of small scale heterogeneity in microbial community abundance in groundwater samples, and we suggest that this may be an intrinsic feature of bore biology. The heterogeneity observed may be driven by bottom up processes (variability in the distribution of organic and inorganic nutrients), top-down processes (grazing and viral lysis), physical heterogeneities in the bore, or technical artifacts associated with the purging process. We suggest that a more detailed understanding of the ecology underpinning this variability is required to adequately describe the microbiological characteristics of groundwater ecosystems.
Collapse
Affiliation(s)
- Ben Roudnew
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | | | | | | | | |
Collapse
|
27
|
Smith RJ, Jeffries TC, Roudnew B, Seymour JR, Fitch AJ, Simons KL, Speck PG, Newton K, Brown MH, Mitchell JG. Confined aquifers as viral reservoirs. Environ Microbiol Rep 2013; 5:725-730. [PMID: 24115623 DOI: 10.1111/1758-2229.12072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
Knowledge about viral diversity and abundance in deep groundwater reserves is limited. We found that the viral community inhabiting a deep confined aquifer in South Australia was more similar to reclaimed water communities than to the viral communities in the overlying unconfined aquifer community. This similarity was driven by high relative occurrence of the single-stranded DNA viral groups Circoviridae, Geminiviridae and Microviridae, which include many known plant and animal pathogens. These groups were present in a 1500-year-old water situated 80 m below the surface, which suggests the potential for long-term survival and spread of potentially pathogenic viruses in deep, confined groundwater. Obtaining a broader understanding of potentially pathogenic viral communities within aquifers is particularly important given the ability of viruses to spread within groundwater ecosystems.
Collapse
Affiliation(s)
- Renee J Smith
- School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Seymour JR, Doblin MA, Jeffries TC, Brown MV, Newton K, Ralph PJ, Baird M, Mitchell JG. Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current. Environ Microbiol Rep 2012; 4:548-555. [PMID: 23760900 DOI: 10.1111/j.1758-2229.2012.00362.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 05/30/2012] [Indexed: 06/02/2023]
Abstract
Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to 'warm-water' ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters.
Collapse
Affiliation(s)
- Justin R Seymour
- Plant Functional Biology & Climate Change Cluster, University of Technology, PO Box 123, Broadway, Sydney, NSW, 2007, Australia
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Smith RJ, Jeffries TC, Roudnew B, Fitch AJ, Seymour JR, Delpin MW, Newton K, Brown MH, Mitchell JG. Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems. Environ Microbiol 2011; 14:240-53. [DOI: 10.1111/j.1462-2920.2011.02614.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Jeffries TC, Seymour JR, Gilbert JA, Dinsdale EA, Newton K, Leterme SSC, Roudnew B, Smith RJ, Seuront L, Mitchell JG. Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS One 2011; 6:e25173. [PMID: 21966446 PMCID: PMC3179486 DOI: 10.1371/journal.pone.0025173] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 08/29/2011] [Indexed: 11/23/2022] Open
Abstract
Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.
Collapse
Affiliation(s)
- Thomas C Jeffries
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|