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Nguyen VH, Wemheuer B, Song W, Bennett H, Webster N, Thomas T. Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species. Syst Appl Microbiol 2023; 46:126426. [PMID: 37141831 DOI: 10.1016/j.syapm.2023.126426] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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2
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Nguyen VH, Wemheuer B, Song W, Bennett H, Palladino G, Burgsdorf I, Sizikov S, Steindler L, Webster NS, Thomas T. Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges. Syst Appl Microbiol 2023; 46:126401. [PMID: 36774720 DOI: 10.1016/j.syapm.2023.126401] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Cawthron Institute, Nelson, New Zealand
| | - Giorgia Palladino
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | | | | | | | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia; Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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3
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Hollensteiner J, Wemheuer F, Schneider D, Pfeiffer B, Wemheuer B. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies. Methods Mol Biol 2023; 2555:13-21. [PMID: 36306076 DOI: 10.1007/978-1-0716-2795-2_2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.
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Affiliation(s)
| | - Franziska Wemheuer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Birgit Pfeiffer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
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Rao S, Esvaran M, Chen L, Kok C, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S. Probiotic supplementation for neonates with congenital gastrointestinal surgical conditions: guidelines for future research. Pediatr Res 2023; 93:49-55. [PMID: 35505080 PMCID: PMC9876795 DOI: 10.1038/s41390-022-02087-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 01/29/2023]
Abstract
Our pilot RCT found that probiotic supplementation with the three-strain bifidobacterial product (B. breve M-16V, B. longum subsp. infantis M-63 and B. longum subsp. longum BB536) attenuates gut dysbiosis, increases stool short-chain fatty acid (SCFA) levels and improves the growth of head circumference in neonates with congenital gastrointestinal surgical conditions (CGISC). In this article, we have provided guidelines for designing future multicentre RCTs based on the experience gained from our pilot RCT. The recommendations include advice about sample size, potential confounders, outcomes of interest, probiotic strain selection, storage, dose, duration and microbial quality assurance, collection of stool samples, storage and analysis and reporting. Following these guidelines will increase the validity of future RCTs in this area and hence confidence in their results. IMPACT: Probiotic supplementation attenuates gut dysbiosis, increases stool short-chain fatty acid (SCFA) levels and improves the growth of head circumference in neonates with congenital gastrointestinal surgical conditions. The current review provides evidence-based guidelines to conduct adequately powered RCTs in this field.
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Affiliation(s)
- Shripada Rao
- Neonatal Intensive Care Unit, Perth Children's Hospital, Perth, WA, Australia. .,Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA, Australia. .,School of Medicine, University of Western Australia, Crawley, WA, Australia.
| | - Meera Esvaran
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia
| | - Liwei Chen
- grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Chooi Kok
- grid.410667.20000 0004 0625 8600Neonatal Intensive Care Unit, Perth Children’s Hospital, Perth, WA Australia ,grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA Australia
| | - Anthony D. Keil
- grid.2824.c0000 0004 0589 6117Department of Microbiology, PathWest Laboratory Medicine, Perth, WA Australia
| | - Ian Gollow
- grid.410667.20000 0004 0625 8600Department of Paediatric Surgery, Perth Children’s Hospital, Perth, WA Australia
| | - Karen Simmer
- grid.410667.20000 0004 0625 8600Neonatal Intensive Care Unit, Perth Children’s Hospital, Perth, WA Australia ,grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Crawley, WA Australia
| | - Bernd Wemheuer
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia ,grid.7450.60000 0001 2364 4210Department of Genomic and Applied Microbiology, University of Göttingen, Göttingen, Germany
| | - Patricia Conway
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia ,grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay Patole
- grid.410667.20000 0004 0625 8600Neonatal Intensive Care Unit, Perth Children’s Hospital, Perth, WA Australia ,grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Crawley, WA Australia
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5
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Taylor JA, Palladino G, Wemheuer B, Steinert G, Sipkema D, Williams TJ, Thomas T. Correction to: Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME J 2022; 16:1200. [PMID: 35042974 PMCID: PMC8940888 DOI: 10.1038/s41396-021-01099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Giorgia Palladino
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.
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Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Dlugosch L, Poehlein A, Wemheuer B, Pfeiffer B, Badewien TH, Daniel R, Simon M. Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nat Commun 2022; 13:456. [PMID: 35075131 PMCID: PMC8786918 DOI: 10.1038/s41467-022-28128-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/06/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial communities are major drivers of global elemental cycles in the oceans due to their high abundance and enormous taxonomic and functional diversity. Recent studies assessed microbial taxonomic and functional biogeography in global oceans but microbial functional biogeography remains poorly studied. Here we show that in the near-surface Atlantic and Southern Ocean between 62°S and 47°N microbial communities exhibit distinct taxonomic and functional adaptations to regional environmental conditions. Richness and diversity showed maxima around 40° latitude and intermediate temperatures, especially in functional genes (KEGG-orthologues, KOs) and gene profiles. A cluster analysis yielded three clusters of KOs but five clusters of genes differing in the abundance of genes involved in nutrient and energy acquisition. Gene profiles showed much higher distance-decay rates than KO and taxonomic profiles. Biotic factors were identified as highly influential in explaining the observed patterns in the functional profiles, whereas temperature and biogeographic province mainly explained the observed taxonomic patterns. Our results thus indicate fine-tuned genetic adaptions of microbial communities to regional biotic and environmental conditions in the Atlantic and Southern Ocean. The taxonomic and functional diversity of marine microbial communities are shaped by both environmental and biotic factors. Here, the authors investigate the functional biogeography of epipelagic prokaryotic communities along a 13,000-km transect in the Southern and Atlantic Oceans, showing finely tuned genetic adaptations to regional conditions.
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Affiliation(s)
- Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Birgit Pfeiffer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Thomas H Badewien
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany. .,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, D-26129, Oldenburg, Germany.
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8
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Rao S, Esvaran M, Chen L, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S. Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial. Pediatr Res 2022; 92:1122-1131. [PMID: 34980887 PMCID: PMC8722408 DOI: 10.1038/s41390-021-01884-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To evaluate whether probiotic supplementation attenuates gut-dysbiosis in neonates with congenital gastrointestinal surgical conditions (CGISC). METHODS Sixty-one neonates (≥35 weeks gestation) with CGISC were randomised to receive daily supplementation with a triple-strain bifidobacterial probiotic (n = 30) or placebo (n = 31) until discharge. Stool microbiota was analysed using 16S ribosomal RNA gene sequencing on samples collected before (T1), 1 week (T2), and 2 weeks (T3) after supplementation and before discharge (T4). The primary outcome was the sum of the relative abundance of potentially pathogenic families of Clostridiaceae, Enterobacteriaceae, Enterococcaceae, Pseudomonaceae, Staphylococcaeae, Streptococcaceae, and Yersiniaceae at T3. RESULTS The median gestational age [38 weeks (IQR: 37.1-38.9)] was similar in both groups. The probiotic group had lower rates of caesarean deliveries (40% versus 70%, p = 0.02). The relative abundance of potentially pathogenic families was lower in the probiotic group compared to placebo at T3 [(median: 50.4 (IQR: 26.6-67.6) versus 67.1 (IQR: 50.9-96.2); p = 0.04). Relative abundance of Bifidobacteriaceae was higher in the probiotic group at T3 [(median: 39.8 (IQR: 24.9-52.1) versus 0.03 (IQR 0.02-2.1); p < 0.001). Stratified analysis continued to show a higher abundance of Bifidobacteriaceae in the probiotic group, irrespective of the mode of delivery. CONCLUSIONS Probiotic supplementation attenuated gut dysbiosis in neonates with CGISC. TRIAL REGISTRATION http://www.anzctr.org.au (ACTRN12617001401347). IMPACT Probiotic supplementation attenuates gut dysbiosis and improves stool short-chain fatty acid levels in neonates with congenital gastrointestinal surgical conditions. This is the second pilot RCT of probiotic supplementation in neonates with congenital gastrointestinal conditions. These findings will pave the way for conducting multicentre RCTs in this area.
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Affiliation(s)
- Shripada Rao
- Neonatal Intensive Care Unit, Perth Children's Hospital, Perth, WA, Australia. .,Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA, Australia. .,School of Medicine, University of Western Australia, Crawley, WA, Australia.
| | - Meera Esvaran
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia
| | - Liwei Chen
- grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Anthony D. Keil
- grid.2824.c0000 0004 0589 6117Department of Microbiology, PathWest Laboratory Medicine, Perth, WA Australia
| | - Ian Gollow
- grid.410667.20000 0004 0625 8600Department of Paediatric Surgery, Perth Children’s Hospital, Perth, WA Australia
| | - Karen Simmer
- grid.410667.20000 0004 0625 8600Neonatal Intensive Care Unit, Perth Children’s Hospital, Perth, WA Australia ,grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Crawley, WA Australia
| | - Bernd Wemheuer
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia ,grid.7450.60000 0001 2364 4210Department of Genomic and Applied Microbiology, University of Göttingen, Göttingen, Germany
| | - Patricia Conway
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia ,grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay Patole
- grid.410667.20000 0004 0625 8600Neonatal Intensive Care Unit, Perth Children’s Hospital, Perth, WA Australia ,grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910School of Medicine, University of Western Australia, Crawley, WA Australia
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9
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Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T. Taxonomic, functional and expression analysis of viral communities associated with marine sponges. PeerJ 2021; 9:e10715. [PMID: 33604175 PMCID: PMC7863781 DOI: 10.7717/peerj.10715] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 08/25/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.
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Affiliation(s)
- Mary Nguyen
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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10
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Tiede J, Diepenbruck M, Gadau J, Wemheuer B, Daniel R, Scherber C. Seasonal variation in the diet of the serotine bat (Eptesicus serotinus): A high-resolution analysis using DNA metabarcoding. Basic Appl Ecol 2020. [DOI: 10.1016/j.baae.2020.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Wemheuer F, Taylor JA, Daniel R, Johnston E, Meinicke P, Thomas T, Wemheuer B. Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiome 2020; 15:11. [PMID: 33902725 PMCID: PMC8067651 DOI: 10.1186/s40793-020-00358-7] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/09/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities. RESULTS To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities. CONCLUSIONS Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.
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Affiliation(s)
- Franziska Wemheuer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Jessica A Taylor
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Emma Johnston
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
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12
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Wemheuer F, Berkelmann D, Wemheuer B, Daniel R, Vidal S, Bisseleua Daghela HB. Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves. Microorganisms 2020; 8:E405. [PMID: 32183118 PMCID: PMC7143032 DOI: 10.3390/microorganisms8030405] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 12/22/2022] Open
Abstract
Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T. cacao and their responsiveness towards agroforestry management systems.
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Affiliation(s)
- Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
| | - Dirk Berkelmann
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Bernd Wemheuer
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany; (D.B.); (B.W.); (R.D.)
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
| | - Hervé Bertin Bisseleua Daghela
- Section of Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany; (F.W.); (H.B.B.D.)
- Laboratory of Entomology, Institute of Agricultural Research for Development (IRAD), BP 2067, Yaoundé, Cameroon
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13
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Rao SC, Esvaran M, Patole SK, Simmer KN, Gollow I, Keil A, Wemheuer B, Chen L, Conway PL. Gut microbiota in neonates with congenital gastrointestinal surgical conditions: a prospective study. Pediatr Res 2020; 88:878-886. [PMID: 32179871 PMCID: PMC7223116 DOI: 10.1038/s41390-020-0824-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND There is limited information on gut microbiota of neonates with congenital gastrointestinal surgical conditions (CGISCs) available. METHODS This study compared stool microbiota and short-chain fatty acids (SCFAs) of 37 term infants with CGISCs with 36 term healthy infants (HIs). Two stool samples were collected from each infant: as soon as possible after birth (week 1) and 10-14 days of life (week 2). RESULTS Bacterial richness and alpha diversity were comparable between CGISCs and HIs at week 1 and week 2 (all p > 0.05). Beta diversity analysis revealed that at week 1, CGISCs had similar community structures to HIs (p = 0.415). However, by week 2, community structures of CGISCs were significantly different from HIs (p = 0.003). At week 1, there were no significant differences in the relative abundances of genera Bifidobacterium and Bacteroides between CGISCs and HIs. At week 2, the relative abundance of Bifidobacterium was significantly lower in CGISCs (mean percentage 7.21 ± 13.49 vs. 28.96 ± 19.6; p = 0.002). Bacteroides were also less abundant in the CGISC group (mean percentage 0.12 ± 0.49 vs. 6.59 ± 8.62; p = 0.039). Relative abundance of genera Pseudomonas and Escherichia-Shigella were higher in CGISCs. At week 2, stool concentrations of all SCFAs were lower in CGISCs (all p < 0.001). CONCLUSIONS During hospitalization, neonates with CGISCs develop gut dysbiosis and deficiency of SCFAs. IMPACT During hospitalisation, neonates with congenital gastrointestinal surgical conditions develop gut dysbiosis with deficiency of Bifidobacteria and Bacteroides and increased abundance of Escherichia-Shigella and Pseudomonas. They also have low levels of short chain fatty acids in their stools compared to healthy infants. This is the first study evaluating the gut microbiota using 16S ribosomal RNA sequencing methods and stool short chain fatty acids in neonates with congenital gastrointestinal surgical conditions and comparing them to healthy infants. The findings of this study will pave the way for randomised trials of bifidobacterial supplementation in neonates with congenital gastrointestinal surgical conditions.
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Affiliation(s)
- Shripada C. Rao
- grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, Perth Children’s Hospital and King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910Centre for Neonatal Research and Education, University of Western Australia, Perth, WA Australia
| | - Meera Esvaran
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia
| | - Sanjay K. Patole
- grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, Perth Children’s Hospital and King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910Centre for Neonatal Research and Education, University of Western Australia, Perth, WA Australia
| | - Karen N. Simmer
- grid.415259.e0000 0004 0625 8678Neonatal Intensive Care Unit, Perth Children’s Hospital and King Edward Memorial Hospital for Women, Perth, WA Australia ,grid.1012.20000 0004 1936 7910Centre for Neonatal Research and Education, University of Western Australia, Perth, WA Australia
| | - Ian Gollow
- grid.410667.20000 0004 0625 8600Department of Paediatric Surgery, Perth Children’s Hospital, Perth, WA Australia
| | - Anthony Keil
- grid.2824.c0000 0004 0589 6117PathWest Laboratory Medicine, Perth, WA Australia
| | - Bernd Wemheuer
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia
| | - Liwei Chen
- grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Patricia L. Conway
- grid.1005.40000 0004 4902 0432Centre for Marine Science and Innovation at the University of New South Wales (UNSW), Sydney, NSW Australia ,grid.59025.3b0000 0001 2224 0361School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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14
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Coffey MJ, Nielsen S, Wemheuer B, Kaakoush NO, Garg M, Needham B, Pickford R, Jaffe A, Thomas T, Ooi CY. Gut Microbiota in Children With Cystic Fibrosis: A Taxonomic and Functional Dysbiosis. Sci Rep 2019; 9:18593. [PMID: 31819107 PMCID: PMC6901462 DOI: 10.1038/s41598-019-55028-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 11/22/2019] [Indexed: 12/30/2022] Open
Abstract
Intestinal dysbiosis has been observed in children with cystic fibrosis (CF), yet the functional consequences are poorly understood. We investigated the functional capacity of intestinal microbiota and inflammation in children with CF. Stool samples were collected from 27 children with CF and 27 age and gender matched healthy controls (HC) (aged 0.8-18 years). Microbial communities were investigated by iTag sequencing of 16S rRNA genes and functional profiles predicted using Tax4Fun. Inflammation was measured by faecal calprotectin and M2-pyruvate kinase. Paediatric CF gastrointestinal microbiota demonstrated lower richness and diversity compared to HC. CF samples exhibited a marked taxonomic and inferred functional dysbiosis when compared to HC. In children with CF, we predicted an enrichment of genes involved in short-chain fatty acid (SCFA), antioxidant and nutrient metabolism (relevant for growth and nutrition) in CF. The notion of pro-inflammatory GI microbiota in children with CF is supported by positive correlations between intestinal inflammatory markers and both genera and functional pathways. We also observed an association between intestinal genera and both growth z-scores and FEV1%. These taxonomic and functional changes provide insights into gastrointestinal disease in children with CF and future gastrointestinal therapeutics for CF should explore the aforementioned pathways and microbial changes.
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Affiliation(s)
- Michael J Coffey
- Discipline of Paediatrics, School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nadeem O Kaakoush
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Millie Garg
- Discipline of Paediatrics, School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Bronwen Needham
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre (MWAC), University of New South Wales, Sydney, NSW, Australia
| | - Adam Jaffe
- Discipline of Paediatrics, School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, High Street, Randwick, NSW, Australia
- Department of Respiratory, Sydney Children's Hospital, High Street, Randwick, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Chee Y Ooi
- Discipline of Paediatrics, School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia.
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, High Street, Randwick, NSW, Australia.
- Department of Gastroenterology, Sydney Children's Hospital, High Street, Randwick, NSW, Australia.
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15
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Langer SG, Gabris C, Einfalt D, Wemheuer B, Kazda M, Bengelsdorf FR. Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters. Microb Biotechnol 2019; 12:1210-1225. [PMID: 30995692 PMCID: PMC6801161 DOI: 10.1111/1751-7915.13409] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 12/14/2017] [Revised: 02/09/2019] [Accepted: 03/29/2019] [Indexed: 01/20/2023] Open
Abstract
Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.
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MESH Headings
- Anaerobiosis
- Archaea/classification
- Archaea/genetics
- Archaea/growth & development
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/growth & development
- Biofuels
- Bioreactors/microbiology
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fungi/classification
- Fungi/genetics
- Fungi/growth & development
- Manure/microbiology
- Metagenomics
- Microbiota
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
| | - Christina Gabris
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
- Present address:
Bühlmann Laboratories AGSchönenbuchSwitzerland
| | - Daniel Einfalt
- Institute of Systematic Botany and EcologyUlm UniversityUlmGermany
- Present address:
Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology & Göttingen Genomics LaboratoryGeorg‐August University GöttingenGöttingenGermany
| | - Marian Kazda
- Institute of Systematic Botany and EcologyUlm UniversityUlmGermany
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16
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Wemheuer F, Wemheuer B, Daniel R, Vidal S. Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands. Sci Rep 2019; 9:14183. [PMID: 31578453 PMCID: PMC6775154 DOI: 10.1038/s41598-019-50540-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/10/2019] [Indexed: 01/04/2023] Open
Abstract
Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A. platanoides. GLA samples of A. campestre and A. platanoides were dominated by Sawadaea polyfida and S. bicornis, respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of A. campestre. Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of A. campestre. This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed Acer species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one Acer species.
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Affiliation(s)
- Franziska Wemheuer
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Stefan Vidal
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany.
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17
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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18
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Ozkan J, Coroneo M, Willcox M, Wemheuer B, Thomas T. Identification and Visualization of a Distinct Microbiome in Ocular Surface Conjunctival Tissue. Invest Ophthalmol Vis Sci 2019; 59:4268-4276. [PMID: 30140925 DOI: 10.1167/iovs.18-24651] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Knowledge of whether microorganisms reside in protected niches of the conjunctiva is potentially significant in terms of minimizing risks of contact lens inflammation/infection and endophthalmitis. We define if and how microbial communities from limbal and forniceal conjunctival tissue differ from those on the conjunctival surface. Methods Human limbal and forniceal conjunctival tissue was obtained from 23 patients undergoing pterygium surgery and analyzed with data from a recent study of conjunctival surface swabs (n = 45). Microbial communities were analyzed by extracting total DNA from tissue samples and surface swabs and sequencing the 16S rRNA gene using the Illumina MiSeq platform. Sequences were quality filtered, clustered into operational taxonomic units (OTUs) at 97% similarity. OTUs associated with blank extraction and sampling negative controls were removed before analysis. Fluorescent in situ hybridization (FISH) was performed on cyrosections of limbal and forniceal conjunctival tissue. Results There was a significant difference in bacterial community structure between the conjunctival surface and fornix (P = 0.001) and limbus (P = 0.001) tissue. No difference was found in bacterial communities between the limbus and fornix (P = 0.764). Fornix and limbal samples were dominated by OTUs classified to the genus Pseudomonas (relative abundance 79.9%), which were found only in low relative abundances on conjunctival surfaces (6.3%). Application of FISH showed the presence of Pseudomonas in the forniceal tissue sample. Conclusions There is a discrete tissue-associated microbiome in freshly-collected human limbal and fornix tissue, which is different from the microbial community structure and composition of the ocular surface microbiome.
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Affiliation(s)
- Jerome Ozkan
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Minas Coroneo
- Department of Ophthalmology, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.,Department of Genomic and Applied Microbiology, University of Göttingen, Göttingen, Germany
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK. The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Front Microbiol 2019; 10:659. [PMID: 31001232 PMCID: PMC6454203 DOI: 10.3389/fmicb.2019.00659] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 12/18/2018] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae, we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter, Paracoccus, and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae-OTUs assigned as “uncultured” were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae-OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.
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Affiliation(s)
- Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Group "Biology of Geological Processes", Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - Heath Mills
- Rhodium Scientific LLC, San Antonio, TX, United States
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States
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Song W, Wemheuer B, Zhang S, Steensen K, Thomas T. MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. Microbiome 2019; 7:36. [PMID: 30832740 PMCID: PMC6399960 DOI: 10.1186/s40168-019-0649-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 05/15/2018] [Accepted: 02/19/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level. RESULTS Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms. CONCLUSION MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .
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Affiliation(s)
- Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Shan Zhang
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Kerrin Steensen
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, Degenhardt J, Engelen B, Daniel R, Wemheuer B. Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean. Archaea 2019; 2019:3717239. [PMID: 31015799 PMCID: PMC6421829 DOI: 10.1155/2019/3717239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/04/2018] [Accepted: 01/08/2019] [Indexed: 01/08/2023]
Abstract
Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.
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Affiliation(s)
- Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Julius Degenhardt
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Lurgi M, Thomas T, Wemheuer B, Webster NS, Montoya JM. Modularity and predicted functions of the global sponge-microbiome network. Nat Commun 2019; 10:992. [PMID: 30824706 PMCID: PMC6397258 DOI: 10.1038/s41467-019-08925-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 05/29/2018] [Accepted: 02/08/2019] [Indexed: 11/10/2022] Open
Abstract
Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.
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Affiliation(s)
- Miguel Lurgi
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS-Paul Sabatier University, 09200, Moulis, France.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, 4816, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jose M Montoya
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS-Paul Sabatier University, 09200, Moulis, France
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Wemheuer B, Thomas T, Wemheuer F. Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes. Microorganisms 2019; 7:E37. [PMID: 30691243 PMCID: PMC6407066 DOI: 10.3390/microorganisms7020037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/26/2022] Open
Abstract
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.
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Affiliation(s)
- Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Division of Agricultural Entomology, Department of Crop Sciences, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
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Ozkan J, Willcox M, Wemheuer B, Wilcsek G, Coroneo M, Thomas T. Biogeography of the human ocular microbiota. Ocul Surf 2019; 17:111-118. [DOI: 10.1016/j.jtos.2018.11.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/22/2018] [Accepted: 11/09/2018] [Indexed: 12/20/2022]
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Wilkes Walburn J, Wemheuer B, Thomas T, Copeland E, O'Connor W, Booth M, Fielder S, Egan S. Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi). Microb Biotechnol 2018; 12:275-288. [PMID: 30506824 PMCID: PMC6389859 DOI: 10.1111/1751-7915.13323] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 11/29/2022] Open
Abstract
The supply of quality juveniles via land-based larviculture represents a major bottleneck to the growing finfish aquaculture industry. As the microbiome plays a key role in animal health, this study aimed to assess the microbial community associated with early larval development of commercially raised Yellowtail Kingfish (Seriola lalandi). We used qPCR and 16S rRNA gene amplicon sequencing to monitor changes in the microbiome associated with the development of S. lalandi from larvae to juveniles. We observed an increase in the bacterial load during larval development, which consisted of a small but abundant core microbiota including taxa belonging to the families Rhodobacteraceae, Lactobacillaceae and Vibrionaceae. The greatest change in the microbiome occurred as larvae moved from a diet of live feeds to formulated pellets, characterized by a transition from Proteobacteria to Firmicutes as the dominant phylum. A prediction of bacterial gene functions found lipid metabolism and secondary metabolite production were abundant in the early larval stages, with carbohydrate and thiamine metabolism functions increasing in abundance as the larvae age and are fed formulated diets. Together, these results suggest that diet is a major contributor to the early microbiome development of commercially raised S. lalandi.
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Affiliation(s)
- Jackson Wilkes Walburn
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth Copeland
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Wayne O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute (PSFI), Taylors Beach, NSW, Australia
| | - Mark Booth
- NSW Department of Primary Industries, Port Stephens Fisheries Institute (PSFI), Taylors Beach, NSW, Australia
| | - Stewart Fielder
- NSW Department of Primary Industries, Port Stephens Fisheries Institute (PSFI), Taylors Beach, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A. Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 2018; 28:348-364. [PMID: 30276908 DOI: 10.1111/mec.14887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 05/16/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/09/2023]
Abstract
Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.
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Affiliation(s)
- Kristina Schröter
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Martin Ehbrecht
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Peter Schall
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Christian Ammer
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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Daniel R, Simon M, Wemheuer B. Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter Clade. Front Microbiol 2018; 9:1185. [PMID: 29910792 PMCID: PMC5992283 DOI: 10.3389/fmicb.2018.01185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia.,School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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Pohlner M, Degenhardt J, von Hoyningen-Huene AJE, Wemheuer B, Erlmann N, Schnetger B, Badewien TH, Engelen B. The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces. Front Microbiol 2017; 8:2550. [PMID: 29326679 PMCID: PMC5741685 DOI: 10.3389/fmicb.2017.02550] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 06/27/2017] [Accepted: 12/08/2017] [Indexed: 01/30/2023] Open
Abstract
By now, only limited information on the Roseobacter group thriving at the seafloor is available. Hence, the current study was conducted to determine their abundance and diversity within Pacific sediments along the 180° meridian. We hypothesize a distinct biogeographical distribution of benthic members of the Roseobacter group linked to nutrient availability within the sediments and productivity of the water column. Lowest cell numbers were counted at the edge of the south Pacific gyre and within the north Pacific gyre followed by an increase to the north with maximum values in the highly productive Bering Sea. Specific quantification of the Roseobacter group revealed on average a relative abundance of 1.7 and 6.3% as determined by catalyzed reported deposition-fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR), respectively. Corresponding Illumina tag sequencing of 16S rRNA genes and 16S rRNA transcripts showed different compositions containing on average 0.7 and 0.9% Roseobacter-affiliated OTUs of the DNA- and RNA-based communities. These OTUs were mainly assigned to uncultured members of the Roseobacter group. Among those with cultured representatives, Sedimentitalea and Sulfitobacter made up the largest proportions. The different oceanic provinces with low nutrient content such as both ocean gyres were characterized by specific communities of the Roseobacter group, distinct from those of the more productive Pacific subarctic region and the Bering Sea. However, linking the community structure to specific metabolic processes at the seafloor is hampered by the dominance of so-far uncultured members of the Roseobacter group, indicating a diversity that has yet to be explored.
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Affiliation(s)
- Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Julius Degenhardt
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Avril J E von Hoyningen-Huene
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Nora Erlmann
- Microbiogeochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernhard Schnetger
- Microbiogeochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thomas H Badewien
- Group "Marine Sensor Systems", Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Wemheuer B, Wemheuer F, Meier D, Billerbeck S, Giebel HA, Simon M, Scherber C, Daniel R. Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea. Microorganisms 2017; 5:microorganisms5040068. [PMID: 29113091 PMCID: PMC5748577 DOI: 10.3390/microorganisms5040068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 09/17/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/16/2022] Open
Abstract
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.
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Affiliation(s)
- Bernd Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Franziska Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Dimitri Meier
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Christoph Scherber
- Institute of Landscape Ecology, University of Muenster, Heisenbergstr. 2, D-48149 Muenster, Germany.
| | - Rolf Daniel
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 2017; 40:370-382. [PMID: 28641923 DOI: 10.1016/j.syapm.2017.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Schall P, Gossner MM, Heinrichs S, Fischer M, Boch S, Prati D, Jung K, Baumgartner V, Blaser S, Böhm S, Buscot F, Daniel R, Goldmann K, Kaiser K, Kahl T, Lange M, Müller J, Overmann J, Renner SC, Schulze ED, Sikorski J, Tschapka M, Türke M, Weisser WW, Wemheuer B, Wubet T, Ammer C. The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12950] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Peter Schall
- Department of Silviculture and Forest Ecology of the Temperate Zones; University of Göttingen; Göttingen Germany
| | - Martin M. Gossner
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; School of Life Sciences Weihenstephan; Technical University of Munich; Freising Germany
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - Steffi Heinrichs
- Department of Silviculture and Forest Ecology of the Temperate Zones; University of Göttingen; Göttingen Germany
| | - Markus Fischer
- Institute of Plant Sciences; University of Bern; Bern Switzerland
| | - Steffen Boch
- Institute of Plant Sciences; University of Bern; Bern Switzerland
| | - Daniel Prati
- Institute of Plant Sciences; University of Bern; Bern Switzerland
| | - Kirsten Jung
- Institute of Evolutionary Ecology and Conservation Genomics; University of Ulm; Ulm Germany
| | - Vanessa Baumgartner
- Leibniz-Institute DSMZ - German Collection of Microorganism and Cell Cultures; Braunschweig Germany
| | - Stefan Blaser
- Institute of Plant Sciences; University of Bern; Bern Switzerland
| | - Stefan Böhm
- Institute of Evolutionary Ecology and Conservation Genomics; University of Ulm; Ulm Germany
| | - François Buscot
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Halle-Saale Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology; University of Göttingen; Göttingen Germany
| | - Kezia Goldmann
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Halle-Saale Germany
| | - Kristin Kaiser
- Department of Genomic and Applied Microbiology; University of Göttingen; Göttingen Germany
| | - Tiemo Kahl
- Silviculture; University of Freiburg; Freiburg Germany
- Biosphere Reserve Vessertal-Thuringian Forest; Schmiedefeld am Rennsteig; Germany
| | - Markus Lange
- Institute of Ecology; Friedrich-Schiller-University; Jena Germany
- Max-Planck Institute for Biogeochemistry; Jena Germany
| | - Jörg Müller
- Department of Biodiversity Research/Systematic Botany; University of Potsdam; Potsdam Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ - German Collection of Microorganism and Cell Cultures; Braunschweig Germany
| | - Swen C. Renner
- Institute of Zoology; University of Natural Resources and Life Sciences; Vienna Austria
- Smithsonian Conservation Biology Institute; National Zoo; Front Royal VA USA
| | | | - Johannes Sikorski
- Leibniz-Institute DSMZ - German Collection of Microorganism and Cell Cultures; Braunschweig Germany
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics; University of Ulm; Ulm Germany
- Smithsonian Tropical Research Institute; Balboa Panama
| | - Manfred Türke
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
- Institute of Ecology; Friedrich-Schiller-University; Jena Germany
- Institute of Biology; Leipzig University; Leipzig Germany
| | - Wolfgang W. Weisser
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; School of Life Sciences Weihenstephan; Technical University of Munich; Freising Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology; University of Göttingen; Göttingen Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Halle-Saale Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Christian Ammer
- Department of Silviculture and Forest Ecology of the Temperate Zones; University of Göttingen; Göttingen Germany
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Granzow S, Kaiser K, Wemheuer B, Pfeiffer B, Daniel R, Vidal S, Wemheuer F. The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment. Front Microbiol 2017; 8:902. [PMID: 28611735 PMCID: PMC5447230 DOI: 10.3389/fmicb.2017.00902] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 06/26/2016] [Accepted: 05/03/2017] [Indexed: 11/24/2022] Open
Abstract
Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.
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Affiliation(s)
- Sandra Granzow
- Section of Agricultural Entomology, Department of Crop Sciences, University of GöttingenGöttingen, Germany
| | - Kristin Kaiser
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Birgit Pfeiffer
- Plant Nutrition and Crop Physiology, Department of Crop Sciences, University of GöttingenGöttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, University of GöttingenGöttingen, Germany
| | - Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, University of GöttingenGöttingen, Germany
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Wöhlbrand L, Wemheuer B, Feenders C, Ruppersberg HS, Hinrichs C, Blasius B, Daniel R, Rabus R. Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea. Front Microbiol 2017; 8:442. [PMID: 28392779 PMCID: PMC5364173 DOI: 10.3389/fmicb.2017.00442] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
Annually recurring phytoplankton spring blooms are characteristic of temperate coastal shelf seas. During these blooms, environmental conditions, including nutrient availability, differ considerably from non-bloom conditions, affecting the entire ecosystem including the bacterioplankton. Accordingly, the emerging ecological niches during bloom transition are occupied by different bacterial populations, with Roseobacter RCA cluster and SAR92 clade members exhibiting high metabolic activity during bloom events. In this study, the functional response of the ambient bacterial community toward a Phaeocystis globosa bloom in the southern North Sea was studied using metaproteomic approaches. In contrast to other metaproteomic studies of marine bacterial communities, this is the first study comparing two different cell lysis and protein preparation methods [using trifluoroethanol (TFE) and in-solution digest as well as bead beating and SDS-based solubilization and in-gel digest (BB GeLC)]. In addition, two different mass spectrometric techniques (ESI-iontrap MS and MALDI-TOF MS) were used for peptide analysis. A total of 585 different proteins were identified, 296 of which were only detected using the TFE and 191 by the BB GeLC method, demonstrating the complementarity of these sample preparation methods. Furthermore, 158 proteins of the TFE cell lysis samples were exclusively detected by ESI-iontrap MS while 105 were only detected using MALDI-TOF MS, underpinning the value of using two different ionization and mass analysis methods. Notably, 12% of the detected proteins represent predicted integral membrane proteins, including the difficult to detect rhodopsin, indicating a considerable coverage of membrane proteins by this approach. This comprehensive approach verified previous metaproteomic studies of marine bacterioplankton, e.g., detection of many transport-related proteins (17% of the detected proteins). In addition, new insights into e.g., carbon and nitrogen metabolism were obtained. For instance, the C1 pathway was more prominent outside the bloom and different strategies for glucose metabolism seem to be applied under the studied conditions. Furthermore, a higher number of nitrogen assimilating proteins were present under non-bloom conditions, reflecting the competition for this limited macro nutrient under oligotrophic conditions. Overall, application of different sample preparation techniques as well as MS methods facilitated a more holistic picture of the marine bacterioplankton response to changing environmental conditions.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Hanna S Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg Oldenburg, Germany
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Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 2017; 7:40914. [PMID: 28102323 PMCID: PMC5244420 DOI: 10.1038/srep40914] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/13/2016] [Indexed: 11/09/2022] Open
Abstract
Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.
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Affiliation(s)
- Franziska Wemheuer
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Kristin Kaiser
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Stefan Vidal
- Section of Agricultural Entomology, Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr. 6, D-37077 Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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Abstract
Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes. The same is true for plant and fungal ITS sequences. The application of highly specific-primers suppressing co-amplification of these sequence contaminations is a good solution for this issue. Here, we describe a detailed protocol for assessing bacterial and fungal endophyte diversity in plants using these primers in combination with next-generation sequencing.
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Affiliation(s)
- Bernd Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Franziska Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
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Schneider D, Wemheuer F, Pfeiffer B, Wemheuer B. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies. Methods Mol Biol 2017; 1539:13-22. [PMID: 27900681 DOI: 10.1007/978-1-4939-6691-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.
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Affiliation(s)
- Dominik Schneider
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Franziska Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Birgit Pfeiffer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Bernd Wemheuer
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
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Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat Microbiol 2016; 1:16063. [PMID: 27572966 DOI: 10.1038/nmicrobiol.2016.63] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/05/2016] [Indexed: 12/13/2022]
Abstract
The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments.
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Affiliation(s)
- Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Sonja Voget
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Lyngby DK-2800 Kgs, Denmark
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida 32514, USA
| | - Rolf Daniel
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
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Wemheuer F, Wemheuer B, Kretzschmar D, Pfeiffer B, Herzog S, Daniel R, Vidal S. Impact of grassland management regimes on bacterial endophyte diversity differs with grass species. Lett Appl Microbiol 2016; 62:323-9. [DOI: 10.1111/lam.12551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 01/02/2016] [Accepted: 01/19/2016] [Indexed: 11/30/2022]
Affiliation(s)
- F. Wemheuer
- Department of Crop Sciences; Georg-August-University Göttingen; Göttingen Germany
| | - B. Wemheuer
- Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - D. Kretzschmar
- Department of Crop Sciences; Georg-August-University Göttingen; Göttingen Germany
| | - B. Pfeiffer
- Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - S. Herzog
- Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - R. Daniel
- Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - S. Vidal
- Department of Crop Sciences; Georg-August-University Göttingen; Göttingen Germany
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Tiede J, Wemheuer B, Traugott M, Daniel R, Tscharntke T, Ebeling A, Scherber C. Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing. PLoS One 2016; 11:e0148781. [PMID: 26859146 PMCID: PMC4747541 DOI: 10.1371/journal.pone.0148781] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 10/17/2015] [Accepted: 01/22/2016] [Indexed: 01/06/2023] Open
Abstract
Plant diversity affects species richness and abundance of taxa at higher trophic levels. However, plant diversity effects on omnivores (feeding on multiple trophic levels) and their trophic and non-trophic interactions are not yet studied because appropriate methods were lacking. A promising approach is the DNA-based analysis of gut contents using next generation sequencing (NGS) technologies. Here, we integrate NGS-based analysis into the framework of a biodiversity experiment where plant taxonomic and functional diversity were manipulated to directly assess environmental interactions involving the omnivorous ground beetle Pterostichus melanarius. Beetle regurgitates were used for NGS-based analysis with universal 18S rDNA primers for eukaryotes. We detected a wide range of taxa with the NGS approach in regurgitates, including organisms representing trophic, phoretic, parasitic, and neutral interactions with P. melanarius. Our findings suggest that the frequency of (i) trophic interactions increased with plant diversity and vegetation cover; (ii) intraguild predation increased with vegetation cover, and (iii) neutral interactions with organisms such as fungi and protists increased with vegetation cover. Experimentally manipulated plant diversity likely affects multitrophic interactions involving omnivorous consumers. Our study therefore shows that trophic and non-trophic interactions can be assessed via NGS to address fundamental questions in biodiversity research.
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Affiliation(s)
- Julia Tiede
- Agroecology, Department of Crop Sciences, Georg-August University Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany
- Institute of Landscape Ecology, University of Muenster, Heisenbergstr. 2, 48149, Muenster, Germany
| | - Bernd Wemheuer
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University Goettingen, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University Goettingen, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Teja Tscharntke
- Agroecology, Department of Crop Sciences, Georg-August University Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany
| | - Anne Ebeling
- Institute of Ecology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Christoph Scherber
- Agroecology, Department of Crop Sciences, Georg-August University Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany
- Institute of Landscape Ecology, University of Muenster, Heisenbergstr. 2, 48149, Muenster, Germany
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Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR. Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. Biotechnol Biofuels 2016; 9:121. [PMID: 27279900 PMCID: PMC4897800 DOI: 10.1186/s13068-016-0534-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood. RESULTS In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample. CONCLUSIONS Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.
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Affiliation(s)
- Simon Güllert
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Martin A. Fischer
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Dmitrij Turaev
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Britta Noebauer
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Nele Ilmberger
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Bernd Wemheuer
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Malik Alawi
- />Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg, Germany
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Thomas Rattei
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Rolf Daniel
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Ruth A. Schmitz
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Adam Grundhoff
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Wolfgang R. Streit
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
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Herzog S, Wemheuer F, Wemheuer B, Daniel R. Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils. PLoS One 2015; 10:e0145575. [PMID: 26694644 PMCID: PMC4687936 DOI: 10.1371/journal.pone.0145575] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 09/27/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application.
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Affiliation(s)
- Sarah Herzog
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Franziska Wemheuer
- Section of Agricultural Entomology, Department for Crop Sciences, Georg-August-University of Göttingen, Grisebachstr. 6, 37077 Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- * E-mail:
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Kanukollu S, Wemheuer B, Herber J, Billerbeck S, Lucas J, Daniel R, Simon M, Cypionka H, Engelen B. Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea. FEMS Microbiol Ecol 2015; 92:fiv145. [PMID: 26607167 DOI: 10.1093/femsec/fiv145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2015] [Indexed: 01/10/2023] Open
Abstract
The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.
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Affiliation(s)
- Saranya Kanukollu
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Bernd Wemheuer
- Georg-August-Universität Göttingen, Genomische und Angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Janina Herber
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Sara Billerbeck
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Judith Lucas
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Rolf Daniel
- Georg-August-Universität Göttingen, Genomische und Angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Meinhard Simon
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Heribert Cypionka
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
| | - Bert Engelen
- Carl-von-Ossietzky Universität Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Straße 9-11, D-26129 Oldenburg, Germany
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Gram L, Rasmussen BB, Wemheuer B, Bernbom N, Ng YY, Porsby CH, Breider S, Brinkhoff T. Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors. Syst Appl Microbiol 2015; 38:483-93. [PMID: 26343311 DOI: 10.1016/j.syapm.2015.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 12/27/2022]
Abstract
Phaeobacter inhibens belongs to the marine Roseobacter clade and is important as a carbon and sulfur metabolizer, a biofilm former and producer of the antibiotic tropodithietic acid (TDA). The majority of cultured strains have been isolated from marine aquaculture sites, however, their niche in the environment is to date unknown. Here, we report on the repeated isolation of Phaeobacter inhibens strains from a marine environment (harbors) not related to aquaculture. Based on phenotype and 16S rRNA gene sequence similarity, a total of 64 P. inhibens strains were identified from 35 samples (eukaryotic organisms or biofilms on inert surfaces) in Jyllinge Harbor during late summer and autumn, but not during winter and spring in 2009, 2011, and 2012. P. inhibens strains were also isolated from biofilms at three other Danish harbors (in 2012), but not from the surrounding seawater. Ten of the 14 samples from which P. inhibens was cultured contained bryozoans. DNA was extracted (in 2012) from 55 out of 74 Jyllinge Harbor samples, and 35 were positive for Phaeobacter using a genus-specific PCR. P. inhibens strains were isolated from nine of these samples. DNA and RNA were isolated from 13 random samples and used for amplification of 16S rRNA. P. inhibens was detected in five of these samples, all of which were biofilm samples, by pyrotag-sequencing at a prevalence of 0.02-0.68% of the prokaryotic community. The results indicated that P. inhibens had a niche in biofilms of fouled surfaces in harbor areas and that the population followed a seasonal fluctuation.
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Affiliation(s)
- Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark.
| | - Bastian Barker Rasmussen
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Bernd Wemheuer
- Georg-August University Göttingen, Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Nete Bernbom
- National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
| | - Yoke Yin Ng
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Cisse H Porsby
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany
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Wemheuer B, Wemheuer F, Hollensteiner J, Meyer FD, Voget S, Daniel R. The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Front Microbiol 2015; 6:805. [PMID: 26322028 PMCID: PMC4531512 DOI: 10.3389/fmicb.2015.00805] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 05/11/2015] [Accepted: 07/22/2015] [Indexed: 12/12/2022] Open
Abstract
Phytoplankton blooms exhibit a severe impact on bacterioplankton communities as they change nutrient availabilities and other environmental factors. In the current study, the response of a bacterioplankton community to a Phaeocystis globosa spring bloom was investigated in the southern North Sea. For this purpose, water samples were taken inside and reference samples outside of an algal spring bloom. Structural changes of the bacterioplankton community were assessed by amplicon-based analysis of 16S rRNA genes and transcripts generated from environmental DNA and RNA, respectively. Several marine groups responded to bloom presence. The abundance of the Roseobacter RCA cluster and the SAR92 clade significantly increased in bloom presence in the total and active fraction of the bacterial community. Functional changes were investigated by direct sequencing of environmental DNA and mRNA. The corresponding datasets comprised more than 500 million sequences across all samples. Metatranscriptomic data sets were mapped on representative genomes of abundant marine groups present in the samples and on assembled metagenomic and metatranscriptomic datasets. Differences in gene expression profiles between non-bloom and bloom samples were recorded. The genome-wide gene expression level of Planktomarina temperata, an abundant member of the Roseobacter RCA cluster, was higher inside the bloom. Genes that were differently expressed included transposases, which showed increased expression levels inside the bloom. This might contribute to the adaptation of this organism toward environmental stresses through genome reorganization. In addition, several genes affiliated to the SAR92 clade were significantly upregulated inside the bloom including genes encoding for proteins involved in isoleucine and leucine incorporation. Obtained results provide novel insights into compositional and functional variations of marine bacterioplankton communities as response to a phytoplankton bloom.
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Affiliation(s)
- Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Franziska Wemheuer
- Department for Crop Sciences, Georg-August-University Göttingen Göttingen, Germany
| | - Jacqueline Hollensteiner
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Frauke-Dorothee Meyer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Sonja Voget
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen Göttingen, Germany
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Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 2015; 31:2882-4. [PMID: 25957349 PMCID: PMC4547618 DOI: 10.1093/bioinformatics/btv287] [Citation(s) in RCA: 845] [Impact Index Per Article: 93.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/03/2015] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. RESULTS Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. AVAILABILITY AND IMPLEMENTATION Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/. CONTACT kasshau@gwdg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany
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Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol 2015; 17:3822-31. [DOI: 10.1111/1462-2920.12842] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Maren A. Seibt
- ICBM-MPI Bridging Group for Marine Geochemistry; Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
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Mientus M, Brady S, Angelov A, Zimmermann P, Wemheuer B, Schuldes J, Daniel R, Liebl W. Thermostable Xylanase and β-Glucanase Derived from the Metagenome of the Avachinsky Crater in Kamchatka (Russia). ACTA ACUST UNITED AC 2013. [DOI: 10.2174/2211550102999131128150257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wemheuer B, Güllert S, Billerbeck S, Giebel HA, Voget S, Simon M, Daniel R. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 2013; 87:378-89. [DOI: 10.1111/1574-6941.12230] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Simon Güllert
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Sara Billerbeck
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Helge-Ansgar Giebel
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Meinhard Simon
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
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