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Article ; Online: Snow viruses and their implications on red snow algal blooms.

Barno, Adam R / Green, Kevin / Rohwer, Forest / Silveira, Cynthia B

mSystems

2024 Volume 9, Issue 5, Page(s) e0008324

Abstract: Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We ... ...

Abstract	Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We hypothesize that these algal blooms affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of double-stranded DNA virus communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Putative snow viruses encoded genes involved in energy metabolisms, such as NAD
MeSH term(s)	Snow/virology ; Snow/microbiology ; British Columbia ; Bacteria/genetics ; Bacteria/virology ; Bacteria/isolation & purification ; Eutrophication ; Genome, Viral/genetics ; Bacteriophages/genetics ; Bacteriophages/isolation & purification ; Rhodophyta/virology ; Viruses/genetics ; Viruses/isolation & purification ; Viruses/classification
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00083-24
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Article: Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles.

Luque, Antoni / Silveira, Cynthia B

mSystems

2020 Volume 5, Issue 5

Abstract: Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing ... ...

Abstract	Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections-a well-understood molecular mechanism of lysogenization-increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates).
Language	English
Publishing date	2020-09-15
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00353-20
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Article: The landscape of lysogeny across microbial community density, diversity and energetics

Silveira, Cynthia B. / Luque, Antoni / Rohwer, Forest

Environmental microbiology. 2021 Aug., v. 23, no. 8

2021

Abstract: Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low‐density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive ... ...

Abstract	Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low‐density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 10⁶ cells ml⁻¹ or g⁻¹) and low diversity, coinfections by two or more phages are frequent and excess energy availability stimulates inefficient metabolism. Both mechanisms favour phage integration and characterize the Piggyback‐the‐Winner dynamic. At low densities (below 10⁵ cells ml⁻¹ or g⁻¹), starvation represses lytic genes and extends the time window for lysogenic commitment, resulting in a higher frequency of coinfections that cause integration. This pattern follows the predictions of the refugium hypothesis. At intermediary densities (between 10⁵ and 10⁶ cells ml⁻¹ or g⁻¹), encounter rates and efficient energy metabolism favour lysis. This may involve Kill‐the‐Winner lytic dynamics and induction. Based on these three regimes, we propose a framework wherein phage integration occurs more frequently at both ends of the host density gradient, with distinct underlying molecular mechanisms (coinfections and host metabolism) dominating at each extreme.
Keywords	bacteriophages ; energy ; energy metabolism ; landscapes ; lysogeny ; microbial communities ; starvation
Language	English
Dates of publication	2021-08
Size	p. 4098-4111.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	REVIEW
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15640
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Article ; Online: The landscape of lysogeny across microbial community density, diversity and energetics.

Silveira, Cynthia B / Luque, Antoni / Rohwer, Forest

Environmental microbiology

2021 Volume 23, Issue 8, Page(s) 4098–4111

Abstract: Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive ... ...

Abstract	Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 10
MeSH term(s)	Bacteria/genetics ; Bacteriophages/genetics ; Lysogeny ; Microbiota
Language	English
Publishing date	2021-06-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15640
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Article: Prophage Genomics and Ecology in the Family

Forcone, Kathryn / Coutinho, Felipe H / Cavalcanti, Giselle S / Silveira, Cynthia B

Microorganisms

2021 Volume 9, Issue 6

Abstract: Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes ... ...

Abstract	Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of
Language	English
Publishing date	2021-05-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms9061115
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Article ; Online: Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.

Coutinho, Felipe H / Silveira, Cynthia B / Sebastián, Marta / Sánchez, Pablo / Duarte, Carlos M / Vaqué, Dolors / Gasol, Josep M / Acinas, Silvia G

Microbiome

2023 Volume 11, Issue 1, Page(s) 118

Abstract: Background: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and ...

Abstract	Background: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts. Results: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. Conclusions: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.
MeSH term(s)	Seawater/microbiology ; Water ; Genes, Viral ; Viruses/genetics ; Microbiota/genetics ; Oceans and Seas
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-05-27
Publishing country	England
Document type	Video-Audio Media ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-023-01547-5
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Article ; Online: Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms.

Hesketh-Best, Poppy J / Bosco-Santos, Alice / Garcia, Sofia L / O'Beirne, Molly D / Werne, Josef P / Gilhooly, William P / Silveira, Cynthia B

Communications earth & environment

2023 Volume 4, Issue 1, Page(s) 126

Abstract: Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By ... ...

Abstract	Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article
ISSN	2662-4435
ISSN (online)	2662-4435
DOI	10.1038/s43247-023-00796-4
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Article ; Online: A mesomelic skeletal dysplasia, Kantaputra-like, not related to HOXD cluster region, and with phenotypic gender differences.

Lacarrubba-Flores, Maria Dora Jazmin / da Costa Silveira, Karina / Silveira, Cynthia / Carvalho, Benilton S / Cavalcanti, Denise Pontes

American journal of medical genetics. Part A

2023 Volume 194, Issue 2, Page(s) 328–336

Abstract: Mesomelic skeletal dysplasia is a heterogeneous group of skeletal disorders that has grown since the molecular basis of these conditions is in the process of research and discovery. Here, we report a Brazilian family with eight affected members over ... ...

Abstract	Mesomelic skeletal dysplasia is a heterogeneous group of skeletal disorders that has grown since the molecular basis of these conditions is in the process of research and discovery. Here, we report a Brazilian family with eight affected members over three generations with a phenotype similar to mesomelic Kantaputra dysplasia. This family presents marked shortening of the upper limbs with hypotrophy of the lower limbs and clubfeet without synostosis. Array-based CNV analysis and exome sequencing of four family members failed to show any region or gene candidate. Interestingly, males were more severely affected than females in this family, suggesting that gender differences could play a role in the phenotypic expressivity of this condition.
MeSH term(s)	Male ; Female ; Humans ; Sex Factors ; Osteochondrodysplasias/genetics ; Family ; Gonadal Dysgenesis ; Phenotype
Language	English
Publishing date	2023-10-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63444
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Zs.A 1376/A: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article: Prophage Genomics and Ecology in the Family Rhodobacteraceae

Forcone, Kathryn / Coutinho, Felipe H. / Cavalcanti, Giselle S. / Silveira, Cynthia B.

Microorganisms. 2021 May 21, v. 9, no. 6

2021

Abstract: Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial ... ...

Abstract	Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
Keywords	Rhodobacter capsulatus ; amino acid metabolism ; carbon ; gene transfer ; genes ; genetic variation ; genomics ; latitude ; lipids ; membrane fluidity ; temperature ; viral genome
Language	English
Dates of publication	2021-0521
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms9061115
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Article ; Online: The coral microbiome in sickness, in health and in a changing world.

Voolstra, Christian R / Raina, Jean-Baptiste / Dörr, Melanie / Cárdenas, Anny / Pogoreutz, Claudia / Silveira, Cynthia B / Mohamed, Amin R / Bourne, David G / Luo, Haiwei / Amin, Shady A / Peixoto, Raquel S

Nature reviews. Microbiology

2024

Abstract: Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and ... ...

Abstract	Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/s41579-024-01015-3
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Zs.A 5865: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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