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Article ; Online: Genome Mining and Evolutionary Analysis Reveal Diverse Type III Polyketide Synthase Pathways in Cyanobacteria.

Larsen, Joachim Steen / Pearson, Leanne Andrea / Neilan, Brett Anthony

2021 Volume 13, Issue 4

Abstract: Cyanobacteria are prolific producers of natural products, including polyketides and hybrid compounds thereof. Type III polyketide synthases (PKSs) are of particular interest, due to their wide substrate specificity and simple reaction mechanism, compared ...

Abstract	Cyanobacteria are prolific producers of natural products, including polyketides and hybrid compounds thereof. Type III polyketide synthases (PKSs) are of particular interest, due to their wide substrate specificity and simple reaction mechanism, compared with both type I and type II PKSs. Surprisingly, only two type III PKS products, hierridins, and (7.7)paracyclophanes, have been isolated from cyanobacteria. Here, we report the mining of 517 cyanobacterial genomes for type III PKS biosynthesis gene clusters. Approximately 17% of the genomes analyzed encoded one or more type III PKSs. Together with already characterized type III PKSs, the phylogeny of this group of enzymes was investigated. Our analysis showed that type III PKSs in cyanobacteria evolved into three major lineages, including enzymes associated with 1) (7.7)paracyclophane-like biosynthesis gene clusters, 2) hierridin-like biosynthesis gene clusters, and 3) cytochrome b5 genes. The evolutionary history of these enzymes is complex, with some sequences partitioning primarily according to speciation and others putatively according to their reaction type. Protein modeling showed that cyanobacterial type III PKSs generally have a smaller active site cavity (mean = 109.035 Å3) compared with enzymes from other organisms. The size of the active site did not correlate well with substrate size, however, the "Gatekeeper" amino acid residues within the active site were strongly correlated to enzyme phylogeny. Our study provides unprecedented insight into the distribution, diversity, and molecular evolution of cyanobacterial type III PKSs, which could facilitate the discovery, characterization, and exploitation of novel enzymes, biochemical pathways, and specialized metabolites from this biosynthetically talented clade of microorganisms.
MeSH term(s)	Biosynthetic Pathways/genetics ; Cyanobacteria/enzymology ; Cyanobacteria/genetics ; Cytochromes b5/genetics ; Data Mining ; Evolution, Molecular ; Genome, Bacterial ; Models, Molecular ; Phylogeny ; Polyketide Synthases/chemistry ; Polyketide Synthases/classification ; Polyketide Synthases/genetics
Chemical Substances	Polyketide Synthases (79956-01-7) ; Cytochromes b5 (9035-39-6)
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evab056
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Heterologous Expression and Biochemical Analysis Reveal a Schizokinen-Based Siderophore Pathway in

Wang, Suqin / Pearson, Leanne A / Mazmouz, Rabia / Liu, Tianzhe / Neilan, Brett A

Applied and environmental microbiology

2022 Volume 88, Issue 7, Page(s) e0237321

Abstract: Siderophores are low molecular weight iron-chelating molecules that many organisms secrete to scavenge ferric iron from the environment. While cyanobacteria inhabit a wide range of environments with poor iron availability, only two siderophore families ... ...

Abstract	Siderophores are low molecular weight iron-chelating molecules that many organisms secrete to scavenge ferric iron from the environment. While cyanobacteria inhabit a wide range of environments with poor iron availability, only two siderophore families have been characterized from this phylum. Herein, we sought to investigate siderophore production in the marine genus,
MeSH term(s)	Chromatography, Liquid ; Cyanobacteria/genetics ; Cyanobacteria/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Humans ; Hydroxamic Acids ; Iron/metabolism ; Siderophores/metabolism ; Tandem Mass Spectrometry
Chemical Substances	Hydroxamic Acids ; Siderophores ; schizokinen (35418-52-1) ; Iron (E1UOL152H7)
Language	English
Publishing date	2022-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.02373-21
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Article ; Online: Recent developments in quantitative PCR for monitoring harmful marine microalgae.

Pearson, Leanne A / D'Agostino, Paul M / Neilan, Brett A

Harmful algae

2021 Volume 108, Page(s) 102096

Abstract: Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including ... ...

Abstract	Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.
MeSH term(s)	Animals ; Dinoflagellida/genetics ; Fisheries ; Microalgae/genetics ; Real-Time Polymerase Chain Reaction ; Shellfish
Language	English
Publishing date	2021-08-30
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2091119-1
ISSN	1878-1470 ; 1568-9883
ISSN (online)	1878-1470
ISSN	1568-9883
DOI	10.1016/j.hal.2021.102096
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Article ; Online: Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies.

Romanis, Caitlin S / Pearson, Leanne A / Neilan, Brett A

Journal of microbiological methods

2020 Volume 180, Page(s) 106123

Abstract: Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled ... ...

Abstract	Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.
MeSH term(s)	Bacterial Toxins ; Bacteriological Techniques/methods ; Cyanobacteria/genetics ; Cyanobacteria/growth & development ; Environmental Monitoring ; Fresh Water/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota ; Proteomics/methods ; Sensitivity and Specificity ; Waste Water/microbiology ; Water Purification/methods
Chemical Substances	Bacterial Toxins ; Waste Water
Language	English
Publishing date	2020-12-13
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	604916-3
ISSN	1872-8359 ; 0167-7012
ISSN (online)	1872-8359
ISSN	0167-7012
DOI	10.1016/j.mimet.2020.106123
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Article ; Online: Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts).

Chilton, Angela M / Nguyen, Suong T T / Nelson, Tiffanie M / Pearson, Leanne A / Neilan, Brett A

Environmental microbiology

2022 Volume 24, Issue 11, Page(s) 5467–5482

Abstract: The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid ... ...

Abstract	The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi-arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.
MeSH term(s)	Soil ; Ecosystem ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Australia ; Microbiota/genetics ; Cyanobacteria/genetics
Chemical Substances	Soil ; RNA, Ribosomal, 16S
Language	English
Publishing date	2022-06-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16098
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Article ; Online: A

Chau, Rocky / Pearson, Leanne A / Cain, Jesse / Kalaitzis, John A / Neilan, Brett A

Applied and environmental microbiology

2021 Volume 87, Issue 6

Abstract: ... ...

Abstract	Pseudoalteromonas
MeSH term(s)	Animals ; Bacterial Proteins/genetics ; Genome, Bacterial ; Octopodiformes/microbiology ; Peptide Synthases/genetics ; Phylogeny ; Polyketide Synthases/genetics ; Pseudoalteromonas/genetics ; Pseudoalteromonas/metabolism ; Secondary Metabolism
Chemical Substances	Bacterial Proteins ; Polyketide Synthases (79956-01-7) ; Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
Language	English
Publishing date	2021-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02604-20
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Article ; Online: Recent developments in quantitative PCR for monitoring harmful marine microalgae

Pearson, Leanne A. / D'Agostino, Paul M. / Neilan, Brett A.

Harmful algae. 2021 Aug., v. 108 p.102096-

2021

Abstract	Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.
Keywords	Miozoa ; algal blooms ; coastal water ; environmental monitoring ; genetic markers ; microalgae ; paralytic shellfish toxins ; phytoplankton ; poisonous algae ; quantitative polymerase chain reaction ; Harmful algal blooms ; Saxitoxin ; rRNA ; Seafood ; sxtA
Language	English
Dates of publication	2021-08
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	2091119-1
ISSN	1878-1470 ; 1568-9883
ISSN (online)	1878-1470
ISSN	1568-9883
DOI	10.1016/j.hal.2021.102096
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes.

Nguyen, Suong T T / Vardeh, David P / Nelson, Tiffanie M / Pearson, Leanne A / Kinsela, Andrew S / Neilan, Brett A

Geobiology

2022 Volume 20, Issue 4, Page(s) 546–559

Abstract: Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from ...

Abstract	Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.
MeSH term(s)	Australia ; Cyanobacteria/genetics ; Geologic Sediments/chemistry ; Lakes/microbiology ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; South Australia
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-03-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2113509-5
ISSN	1472-4669 ; 1472-4677
ISSN (online)	1472-4669
ISSN	1472-4677
DOI	10.1111/gbi.12489
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Article ; Online: Mutagenesis of the Microcystin Tailoring and Transport Proteins in a Heterologous Cyanotoxin Expression System.

Liu, Tianzhe / Mazmouz, Rabia / Pearson, Leanne A / Neilan, Brett A

ACS synthetic biology

2019 Volume 8, Issue 5, Page(s) 1187–1194

Abstract: The microcystins are a large group of cyclic peptide hepatotoxins produced by several genera of freshwater cyanobacteria. The genes responsible for microcystin biosynthesis are encoded within a large (∼55 kbp) gene cluster, mcyA-J. The recent ... ...

Abstract	The microcystins are a large group of cyclic peptide hepatotoxins produced by several genera of freshwater cyanobacteria. The genes responsible for microcystin biosynthesis are encoded within a large (∼55 kbp) gene cluster, mcyA-J. The recent establishment of a cyanotoxin heterologous expression system in Escherichia coli has provided the means to study microcystin biosynthesis in a genetically tractable, rapidly growing host. Using this system, we demonstrate that deletion of the ABC-transporter, mcyH, and dehydrogenase, mcyI, abolishes microcystin production, while deletion of the O-methyltransferase, mcyJ, results in the production of the demethylated (DM) toxin [d-Asp
MeSH term(s)	ATP-Binding Cassette Transporters/genetics ; ATP-Binding Cassette Transporters/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Chromatography, High Pressure Liquid ; Escherichia coli/metabolism ; Microcystins/analysis ; Microcystins/chemistry ; Microcystins/metabolism ; Multigene Family ; Mutagenesis ; Protein O-Methyltransferase/deficiency ; Protein O-Methyltransferase/genetics ; Tandem Mass Spectrometry
Chemical Substances	ATP-Binding Cassette Transporters ; Bacterial Proteins ; Microcystins ; microcystin (77238-39-2) ; Protein O-Methyltransferase (EC 2.1.1.-)
Language	English
Publishing date	2019-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.9b00068
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Article ; Online: Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts)

Chilton, Angela M. / Nguyen, Suong T. T. / Nelson, Tiffanie M. / Pearson, Leanne A. / Neilan, Brett A.

Environmental Microbiology. 2022 Nov., v. 24, no. 11 p.5467-5482

2022

Abstract: The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or ‘biocrusts’. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi‐arid ... ...

Abstract	The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or ‘biocrusts’. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi‐arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi‐arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.
Keywords	Actinobacteria ; Bacteroidetes ; Chloroflexi ; Microcoleus ; Proteobacteria ; arid lands ; biological soil crusts ; climate ; climate change ; community structure ; ecosystems ; genetic variation ; microbial communities ; microbiology ; microbiome ; rain ; summer ; Australia
Language	English
Dates of publication	2022-11
Size	p. 5467-5482.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16098
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