Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand

Secker, Nick H.; Chua, Jocelyn P.S.; Laurie, Rebecca E.; McNoe, Les; Guy, P. L.; Orlovich, David A.; Summerfield, Tina C.

doi:10.1111/jpy.12434

Cited by 19 publications

(21 citation statements)

References 62 publications

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“…3). Such diversity is consistent with that of other nonaxenic cyanobacteria from different environments (46)(47)(48)(49)(50), where both free and attached bacteria have been associated with cyanobacterial filaments (47,50). Although the explicit identity of bacteria firmly attached in the SEM images (Fig.…”

Section: Discussionsupporting

confidence: 87%

Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

Hughes

Zhang

et al. 2017

Appl Environ Microbiol

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The cyanobacterial culture HT-58-2 was originally described as a strain of with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with strains and not with isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by, 97% of which are species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll, and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis. A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway.

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Section: Discussionsupporting

confidence: 87%

Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

Hughes

Zhang

et al. 2017

Appl Environ Microbiol

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“…We considered all bacterial taxa these authors had inferred to be closely associated with Nostoc , whether localized to the inner gelatinous matrix or on the outer surface of the colony, even though our microscopic observations, like those of New Zealand wetland Nostoc colonies (Secker et al. 2016), did not reveal many bacteria in the gelatinous matrix. Our 16S rRNA gene sequences for Parinacota Nostoc indicated several bacterial genera in common with those inferred for northern Chilean Altiplano lake or stream Nostoc by Aguilar et al.…”

Section: Discussionmentioning

confidence: 99%

“…Subsequently, epimicrobiota of Nostoc sampled from New Zealand wetlands were inferred from 16S rRNA gene amplicons and light microscopy (Secker et al. 2016), and such amplicons were also employed to characterize host taxonomic relationships and bacterial communities associated with lake and stream Nostoc sampled from the Altiplano of northern Chile (Aguilar et al. 2019).…”

mentioning

confidence: 99%

Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria)

Satjarak

Graham

Piotrowski

et al. 2020

Journal of Phycology

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Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free‐living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.

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“…However, application of molecular taxonomical methods revealed associated bacteria in macroscopic Nostoc sp. colonies [30], and therefore such colonies should be considered as multispecies consortia. Nostoc sp.…”

Section: Introductionmentioning

confidence: 99%

Internal structure and photosynthetic performance of Nostoc sp. colonies in the high Arctic

Kvíderová

2018

Acta Soc Bot Pol

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The physiological performance of <em>Nostoc</em> sp. colonies in the high Arctic was investigated based on their structure and function. To investigate the internal colony structure, a method based on vertical stacking of individual light microscopy images was tested under the conditions at a polar field station. The physiological state of sun-exposed and shaded surfaces of the colonies was assessed using variable chlorophyll fluorescence imaging under two distinct low- and high-light conditions. The 3D image of the internal structure of the colonies revealed a high number of cells in the central part of the colony. Two peaks of maximum cell density were observed, probably caused by two overlapping colony lobes or subcolonies. Light was the driving factor of photosynthetic activity, and the colony structure played a role in the rate of response to incoming light. Fluorescence imaging revealed heterogeneity of the photosynthetic activity in the colonies, with the maximum photosynthetic activity at the colony edge due to better access to nutrients. The differences between exposed and shaded surfaces were not as pronounced as was expected, either due to good photoacclimation to a broad range of light conditions, light distribution through translucent extracellular matrixes, or integration of fluorescence signals throughout the colonies. The slightly better photosynthetic performance under high light conditions may indicate photoacclimation of <em>Nostoc</em> sp. to a broad range of light conditions encountered in the field.

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Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand

Cited by 19 publications

References 62 publications

Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria)

Internal structure and photosynthetic performance of Nostoc sp. colonies in the high Arctic

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