Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O
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            Cyanobacterial Mat Community

Grim, Sharon L.; Voorhies, Alexander A.; Biddanda, Bopaiah A.; Jain, Sunit; Nold, Stephen C.; Green, Russ; Dick, Gregory J.

doi:10.1128/msystems.01042-21

Cited by 8 publications

(10 citation statements)

References 110 publications

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“…We used protein sequences predicted from previously generated metagenomes (Grim et al, 2021; Voorhies et al, 2016) to identify proteins, and metagenome-assembled genomic bins refined through anvi’o (Eren et al, 2015) to link proteins to specific organisms. Briefly, we used ‘anvi-gen-contigs-database’ to profile the metagenomic co-assembly of 15 samples from 2007-2012.…”

Section: Methodsmentioning

confidence: 99%

“…The Middle Island Sinkhole (MIS) in Lake Huron hosts extensive cyanobacterial mat communities that sit at an O 2 /H 2 S interface and switch between oxygenic and anoxygenic photosynthesis depending on supply of sulfide (Kinsman-Costello et al, 2017; Voorhies et al, 2012). The cyanobacterium Phormidium dominates the metatranscriptome and metagenome with genes for AP in a variably sulfidic environment and OP in microaerobic conditions (Grim et al, 2021). The mats are bathed in low-oxygen, high-sulfate groundwater that has relatively stable temperature throughout the year (Ruberg et al, 2008), providing an opportunity to study the relationship between seasonal changes in light and groundwater chemistry and microbial community composition and function.…”

Section: Introductionmentioning

confidence: 99%

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Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Grim

Stuart

Aron

et al. 2023

Preprint

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Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulfide by altering the balance of oxygenic photosynthesis and sulfide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in Middle Island Sinkhole (MIS), where anoxic and sulfate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulfur-oxidizing bacteria, and sulfate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulfur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulfur oxidizers and sulfate reducers, sulfate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulfur and O2 in cyanobacterial mats.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Grim

Stuart

Aron

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We used protein sequences predicted from previously generated metagenomes (Grim et al, 2021; Voorhies et al, 2016) to identify proteins, and metagenome‐assembled genomic bins refined through anvi'o (Eren et al, 2015) to link proteins to specific organisms. Analysis of the metagenome‐assembled genomic bins (MAGs) is described in Grim et al (2021). Our oscillatorial cyanobacterial bins had 70.4% completion/56.3% redundancy ( Phormidium , 11.0 Mbp), 91.6%/42.3% ( Planktothrix , 5.7 Mbp), 95.8%/11.3% ( Pseudanabaena , 4.3 Mbp), and 22.5%/1.41% ( Spirulina , 1.1 Mbp), as well as a 527 Kbp collection of cyanobacterial scaffolds that were not able to be confidently binned.…”

Section: Methodsmentioning

confidence: 99%

Seasonal shifts in community composition and proteome expression in a sulphur‐cycling cyanobacterial mat

Grim,

Stuart,

Aron

et al. 2023

Environmental Microbiology

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Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide‐driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate‐rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur‐oxidizing bacteria, and sulphate‐reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light‐harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O2 in cyanobacterial mats.

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“…Extant microbial mats in Lake Huron's Middle Island Sinkhole (MIS) are composed of cyanobacteria, diatoms, and chemosynthetic sulfur-oxidizing bacteria that cover the floor and walls of the submerged sinkhole (Biddanda et al, 2012;Nold, Pangborn, et al, 2010;Voorhies et al, 2012). Previous work on the composition of the primary producer community in the upper layers of the MIS mat ecosystem revealed relatively depauperate cyanobacterial types corresponding to the form-genera "Phormidium" and "Oscillatoria" (e.g., Biddanda et al, 2015;Grim et al, 2021;Snider et al, 2017). The prevailing consensus has been that the sinkhole mat cyanobacteria are functionally versatile, but with low genetic and phenotypic diversity (Biddanda et al, 2012;Nold, Pangborn, et al, 2010;Voorhies et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (cyanobacteria)

McGovern

Norwich

Thomas

et al. 2023

Journal of Phycology

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Cyanobacteria are diverse prokaryotic, photosynthetic organisms present in nearly every known ecosystem. Recent investigations around the world have recovered vast amounts of novel biodiversity in seldom sampled habitats. One phylogenetically significant character, the secondary folding structures of the 16S–23S ITS rDNA region, has allowed an unprecedented capacity to erect new species. However, two questions arise: Is this feature as informative as is proposed, and how do we best employ these features? Submerged sinkholes with oxygen‐poor, sulfur‐rich ground water in Lake Huron (USA) contain microbial mats dominated by both oxygenic and anoxygenic cyanobacteria. We sought to document some of this unique cyanobacterial diversity. Using culture‐based investigations, we recovered 45 strains, of which 23 were analyzed employing 16S–23S rDNA sequences, ITS folding patterns, ecology, and morphology. With scant morphological discontinuities and nebulous 16S rDNA gene sequence divergence, ITS folding patterns were effective at articulating cryptic biodiversity. However, we would have missed these features had we not folded all the available motifs from the strains, including those with highly similar 16S rDNA gene sequences. If we had relied solely on morphological or 16S rDNA gene data, then we might well have missed the diversity of Anagnostidinema. Thus, in order to avoid conformation basis, which is potentially common when employing ITS structures, we advocate clustering strains based on ITS rDNA region patterns independently and comparing them back to 16S rDNA gene phylogenies. Using a total evidence approach, we erected a new taxon according to the International Code of Nomenclature for Algae, Fungi, and Plants: Anagnostidinema visiae.

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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O ₂ Cyanobacterial Mat Community

Cited by 8 publications

References 110 publications

Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Seasonal shifts in community composition and proteome expression in a sulphur‐cycling cyanobacterial mat

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (cyanobacteria)

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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community

Cited by 8 publications

References 110 publications

Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat

Seasonal shifts in community composition and proteome expression in a sulphur‐cycling cyanobacterial mat

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (cyanobacteria)

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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O ₂ Cyanobacterial Mat Community