1
|
Alathari S, Chaput DL, Bolaños LM, Joseph A, Jackson VLN, Verner-Jeffreys D, Paley R, Tyler CR, Temperton B. Correction: Alathari et al. A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia. Viruses 2023, 15, 965. Viruses 2023; 15:1476. [PMID: 37515305 PMCID: PMC10321574 DOI: 10.3390/v15071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/30/2023] Open
Abstract
In the original publication [...].
Collapse
Affiliation(s)
- Shayma Alathari
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Dominique L Chaput
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Luis M Bolaños
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Joseph
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
| | - Victoria L N Jackson
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - David Verner-Jeffreys
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
- Sustainable Aquaculture Futures Centre, University of Exeter, Exeter EX4 4QD, UK
| | - Richard Paley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
| | - Charles R Tyler
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
- Sustainable Aquaculture Futures Centre, University of Exeter, Exeter EX4 4QD, UK
| | - Ben Temperton
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| |
Collapse
|
2
|
Alathari S, Chaput DL, Bolaños LM, Joseph A, Jackson VLN, Verner-Jeffreys D, Paley R, Tyler CR, Temperton B. A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia. Viruses 2023; 15:v15040965. [PMID: 37112945 PMCID: PMC10145788 DOI: 10.3390/v15040965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Tilapia farming is one of the most important sectors in aquaculture worldwide and of major importance to global food security. Infectious spleen and kidney necrosis virus (ISKNV) has been identified as an agent of high morbidity and mortality, threatening tilapia aquaculture. ISKNV was detected in Lake Volta, Ghana, in September 2018 and spread rapidly, with mortality rates between 60 and 90% and losses of more than 10 tonnes of fish per day. Understanding the spread and evolution of viral pathogens is important for control strategies. Here, we developed a tiled-PCR sequencing approach for the whole-genome sequencing of ISKNV, using long read sequencing to enable field-based, real-time genomic surveillance. This work represents the first use of tiled-PCR for whole genome recovery of viruses in aquaculture, with the longest genome target (>110 kb dsDNA) to date. Our protocol was applied to field samples collected from the ISKNV outbreaks from four intensive tilapia cage culture systems across Lake Volta, between October 2018 and May 2022. Despite the low mutation rate of dsDNA viruses, 20 single nucleotide polymorphisms accumulated during the sampling period. Droplet digital PCR identified a minimum requirement of template in a sample to recover 50% of an ISKNV genome at 275 femtograms (2410 viral templates per 5 µL sequencing reaction). Overall, tiled-PCR sequencing of ISKNV provides an informative tool to assist in disease control in aquaculture.
Collapse
Affiliation(s)
- Shayma Alathari
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Dominique L Chaput
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Luis M Bolaños
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Joseph
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
| | - Victoria L N Jackson
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - David Verner-Jeffreys
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
- Sustainable Aquaculture Futures Centre, University of Exeter, Exeter EX4 4QD, UK
| | - Richard Paley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Barrack Road, Weymouth DT4 8UB, UK
| | - Charles R Tyler
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
- Sustainable Aquaculture Futures Centre, University of Exeter, Exeter EX4 4QD, UK
| | - Ben Temperton
- Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| |
Collapse
|
3
|
Arróniz-Crespo M, Bougoure J, Murphy DV, Cutler NA, Souza-Egipsy V, Chaput DL, Jones DL, Ostle N, Wade SC, Clode PL, DeLuca TH. Revealing the transfer pathways of cyanobacterial-fixed N into the boreal forest through the feather-moss microbiome. Front Plant Sci 2022; 13:1036258. [PMID: 36570951 PMCID: PMC9780503 DOI: 10.3389/fpls.2022.1036258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Biological N2 fixation in feather-mosses is one of the largest inputs of new nitrogen (N) to boreal forest ecosystems; however, revealing the fate of newly fixed N within the bryosphere (i.e. bryophytes and their associated organisms) remains uncertain. METHODS Herein, we combined 15N tracers, high resolution secondary ion mass-spectrometry (NanoSIMS) and a molecular survey of bacterial, fungal and diazotrophic communities, to determine the origin and transfer pathways of newly fixed N2 within feather-moss (Pleurozium schreberi) and its associated microbiome. RESULTS NanoSIMS images reveal that newly fixed N2, derived from cyanobacteria, is incorporated into moss tissues and associated bacteria, fungi and micro-algae. DISCUSSION These images demonstrate that previous assumptions that newly fixed N2 is sequestered into moss tissue and only released by decomposition are not correct. We provide the first empirical evidence of new pathways for N2 fixed in feather-mosses to enter the boreal forest ecosystem (i.e. through its microbiome) and discuss the implications for wider ecosystem function.
Collapse
Affiliation(s)
- María Arróniz-Crespo
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- School of Agricultural Engineering, CEIGRAM, Universidad Politecnica de Madrid, Madrid, Spain
| | - Jeremy Bougoure
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Daniel V. Murphy
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Nick A. Cutler
- Department of Geography, Scott Polar Research Institute, Cambridge, United Kingdom
- School of Geography, Politics and Sociology, Newcastle University, Newcastle, United Kingdom
| | - Virginia Souza-Egipsy
- Servicio de Microscopıa Electronica, Instituto Ciencias Agrarias CSIC, Madrid, Spain
| | | | - Davey L. Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Nicholas Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Stephen C. Wade
- Advanced Microscopy and Bioimaging, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Thomas H. DeLuca
- Department of Forest Ecosystems & Society, College of Forestry, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
4
|
Thornber K, Bashar A, Ahmed MS, Bell A, Trew J, Hasan M, Hasan NA, Alam MM, Chaput DL, Haque MM, Tyler CR. Antimicrobial Resistance in Aquaculture Environments: Unravelling the Complexity and Connectivity of the Underlying Societal Drivers. Environ Sci Technol 2022; 56:14891-14903. [PMID: 36102785 PMCID: PMC9631993 DOI: 10.1021/acs.est.2c00799] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 05/26/2023]
Abstract
Food production environments in low- and middle-income countries (LMICs) are recognized as posing significant and increasing risks to antimicrobial resistance (AMR), one of the greatest threats to global public health and food security systems. In order to maximize and expedite action in mitigating AMR, the World Bank and AMR Global Leaders Group have recommended that AMR is integrated into wider sustainable development strategies. Thus, there is an urgent need for tools to support decision makers in unravelling the complex social and environmental factors driving AMR in LMIC food-producing environments and in demonstrating meaningful connectivity with other sustainable development issues. Here, we applied the Driver-Pressure-State-Impact-Response (DPSIR) conceptual framework to an aquaculture case study site in rural Bangladesh, through the analysis of distinct social, microbiological, and metagenomic data sets. We show how the DPSIR framework supports the integration of these diverse data sets, first to systematically characterize the complex network of societal drivers of AMR in these environments and second to delineate the connectivity between AMR and wider sustainable development issues. Our study illustrates the complexity and challenges of addressing AMR in rural aquaculture environments and supports efforts to implement global policy aimed at mitigating AMR in aquaculture and other rural LMIC food-producing environments.
Collapse
Affiliation(s)
- Kelly Thornber
- Biosciences,
Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United
Kingdom
- Centre
for Sustainable Aquaculture Futures, University
of Exeter, Stocker Road, Exeter EX4
4QD, United Kingdom
| | - Abul Bashar
- Department
of Aquaculture, Bangladesh Agricultural
University, Mymensingh 2202, Bangladesh
| | | | - Ashley Bell
- Biosciences,
Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United
Kingdom
| | - Jahcub Trew
- Biosciences,
Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United
Kingdom
| | - Mahmudul Hasan
- Department
of Aquaculture, Bangladesh Agricultural
University, Mymensingh 2202, Bangladesh
| | - Neaz A. Hasan
- Department
of Aquaculture, Bangladesh Agricultural
University, Mymensingh 2202, Bangladesh
| | - Md. Mehedi Alam
- Department
of Aquaculture, Bangladesh Agricultural
University, Mymensingh 2202, Bangladesh
| | - Dominique L. Chaput
- Biosciences,
Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United
Kingdom
| | | | - Charles R. Tyler
- Biosciences,
Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United
Kingdom
- Centre
for Sustainable Aquaculture Futures, University
of Exeter, Stocker Road, Exeter EX4
4QD, United Kingdom
| |
Collapse
|
5
|
Zeiner CA, Purvine SO, Zink E, Wu S, Paša-Tolić L, Chaput DL, Santelli CM, Hansel CM. Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition. Front Microbiol 2021; 12:610497. [PMID: 33643238 PMCID: PMC7902709 DOI: 10.3389/fmicb.2021.610497] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/26/2020] [Accepted: 01/11/2021] [Indexed: 02/03/2023] Open
Abstract
Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.
Collapse
Affiliation(s)
- Carolyn A Zeiner
- Department of Biology, University of St. Thomas, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika Zink
- Biological Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, OK, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dominique L Chaput
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Cara M Santelli
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Colleen M Hansel
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| |
Collapse
|
6
|
Chaput DL, Bass D, Alam MM, Al Hasan N, Stentiford GD, van Aerle R, Moore K, Bignell JP, Haque MM, Tyler CR. The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh. Viruses 2020; 12:v12030258. [PMID: 32120863 PMCID: PMC7150994 DOI: 10.3390/v12030258] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/26/2022] Open
Abstract
Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.
Collapse
Affiliation(s)
- Dominique L. Chaput
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
- Correspondence: (D.L.C.); (C.R.T.); Tel.: +44-(0)-1392-724450 (C.R.T.)
| | - David Bass
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Md. Mehedi Alam
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Neaz Al Hasan
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK;
| | - John P. Bignell
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Mohammad Mahfujul Haque
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Charles R. Tyler
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- Correspondence: (D.L.C.); (C.R.T.); Tel.: +44-(0)-1392-724450 (C.R.T.)
| |
Collapse
|
7
|
Cutler NA, Arróniz-Crespo M, Street LE, Jones DL, Chaput DL, DeLuca TH. Correction to: Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance. Microb Ecol 2020; 79:516. [PMID: 31286169 DOI: 10.1007/s00248-019-01408-5] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The original version of this article contained an error in the Molecular Analysis subsection of the Methods.
Collapse
Affiliation(s)
- Nick A Cutler
- Scott Polar Research Institute, Lensfield Road, Cambridge, CB2 1EP, UK.
- School of Geography, Politics and Sociology, Newcastle University, Newcastle, NE1 7RU, UK.
| | - María Arróniz-Crespo
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Lorna E Street
- Terrestrial Environmental Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - David L Jones
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Dominique L Chaput
- Department of Mineral Sciences, Smithsonian Institution, National Museum of Natural History, 10th & Constitution NW, Washington, DC, 20560-119, USA
| | - Thomas H DeLuca
- School of Environment and Forest Science, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
8
|
Zeiner CA, Purvine SO, Zink EM, Paša-Tolić L, Chaput DL, Wu S, Santelli CM, Hansel CM. Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi. Fungal Genet Biol 2017; 106:61-75. [DOI: 10.1016/j.fgb.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 01/05/2023]
|
9
|
Cutler NA, Arróniz-Crespo M, Street LE, Jones DL, Chaput DL, DeLuca TH. Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance. Microb Ecol 2017; 73:75-90. [PMID: 27538873 DOI: 10.1007/s00248-016-0832-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Our study used a ∼360-year fire chronosequence in northern Sweden to investigate post-fire microbial community dynamics in the boreal bryosphere (the living and dead parts of the feather moss layer on the forest floor, along with the associated biota). We anticipated systematic changes in microbial community structure and growth strategy with increasing time since fire (TSF) and used amplicon pyrosequencing to establish microbial community structure. We also recorded edaphic factors (relating to pH, C and N accumulation) and the physical characteristics of the feather moss layer. The molecular analyses revealed an unexpectedly diverse microbial community. The structure of the community could be largely explained by just two factors, TSF and pH, although the importance of TSF diminished as the forest recovered from disturbance. The microbial communities on the youngest site (TSF = 14 years) were clearly different from older locations (>100 years), suggesting relatively rapid post-fire recovery. A shift towards Proteobacterial taxa on older sites, coupled with a decline in the relative abundance of Acidobacteria, suggested an increase in resource availability with TSF. Saprotrophs dominated the fungal community. Mycorrhizal fungi appeared to decline in abundance with TSF, possibly due to changing N status. Our study provided evidence for the decadal-scale legacy of burning, with implications for boreal forests that are expected to experience more frequent burns over the course of the next century.
Collapse
Affiliation(s)
- Nick A Cutler
- Scott Polar Research Institute, Lensfield Road, Cambridge, CB2 1EP, UK.
- Churchill College, Cambridge, CB3 0DS, UK.
| | - María Arróniz-Crespo
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Lorna E Street
- Terrestrial Environmental Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - David L Jones
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Dominique L Chaput
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, 10th & Constitution NW, Washington, DC, 20560-119, USA
| | - Thomas H DeLuca
- School of Environment and Forest Science, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
10
|
Zeiner CA, Purvine SO, Zink EM, Paša-Tolić L, Chaput DL, Haridas S, Wu S, LaButti K, Grigoriev IV, Henrissat B, Santelli CM, Hansel CM. Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi. PLoS One 2016; 11:e0157844. [PMID: 27434633 PMCID: PMC4951024 DOI: 10.1371/journal.pone.0157844] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/06/2016] [Indexed: 01/08/2023] Open
Abstract
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
Collapse
Affiliation(s)
- Carolyn A. Zeiner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Erika M. Zink
- Biological Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Dominique L. Chaput
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, Centre National de la Recherche Scientifique and Aix-Marseille Université, 13288 Marseille Cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Cara M. Santelli
- Department of Earth Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Colleen M. Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
11
|
Abstract
Microbial biofilms are common on lithic surfaces, including stone buildings. However, the ecology of these communities is poorly understood. Few studies have focused on the spatial characteristics of lithobiontic biofilms, despite the fact that spatial structure has been demonstrated to influence ecosystem function (and hence biodegradation) and community diversity. Furthermore, relatively few studies have utilized molecular techniques to characterize these communities, even though molecular methods have revealed unexpected microbial diversity in other habitats. This study investigated (1) the spatial structure and (2) the taxonomic composition of an epilithic biofilm using molecular techniques, namely amplicon pyrosequencing and terminal restriction fragment length polymorphism. Dispersion indices and Mantel correlograms were used to test for the presence of spatial structure in the biofilm. Diversity metrics and rank-abundance distributions (RADs) were also generated. The study revealed spatial structure on a centimetre scale in eukaryotic microbes (fungi and algae), but not the bacteria. Fungal and bacterial communities were highly diverse; algal communities much less so. The RADs were characterized by a distinctive 'hollow' (concave up) profile and long tails of rare taxa. These findings have implications for understanding the ecology of epilithic biofilms and the spatial heterogeneity of stone biodeterioration.
Collapse
Affiliation(s)
- Nick A Cutler
- Geography Department, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK
| | - Dominique L Chaput
- Department of Mineral Sciences, Smithsonian Institution, National Museum of Natural History, 10 & Constitution NW, Washington, DC 20560-119, USA
| | - Anna E Oliver
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, UK
| | - Heather A Viles
- School of Geography and the Environment, Oxford University Centre for the Environment, South Parks Road, Oxford OX1 3QY, UK
| |
Collapse
|