Taxonomic, functional and expression analysis of viral communities associated with marine sponges

Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.

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Sexual dimorphism in a top predator ( Notophthalmus viridescens ) drives aquatic prey community assembly

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.1717 ◽

2018 ◽

Vol 285 (1890) ◽

pp. 20181717 ◽

Cited By ~ 7

Author(s):

Denon Start ◽

Stephen De Lisle

Keyword(s):

Sexual Dimorphism ◽

Sex Ratio ◽

Intraspecific Variation ◽

Structure And Function ◽

Sexually Dimorphic ◽

Ecological Communities ◽

Top Predator ◽

Aquatic Mesocosms ◽

And Function ◽

The Impact

Intraspecific variation can have important consequences for the structure and function of ecological communities, and serves to link community ecology to evolutionary processes. Differences between the sexes are an overwhelmingly common form of intraspecific variation, but its community-level consequences have never been experimentally investigated. Here, we manipulate the sex ratio of a sexually dimorphic predacious newt in aquatic mesocosms, then track their impact on prey communities. Female and male newts preferentially forage in the benthic and pelagic zones, respectively, causing corresponding reductions in prey abundances in those habitats. Sex ratio differences also explained a large proportion (33%) of differences in the composition of entire pond communities. Ultimately, we demonstrate the impact of known patterns of sexual dimorphism in a predator on its prey, uncovering overlooked links between evolutionary adaptation and the structure of contemporary communities. Given the extreme prevalence of sexual dimorphism, we argue that the independent evolution of the sexes will often have important consequences for ecological communities.

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

10.1101/2020.06.29.177501 ◽

2020 ◽

Cited By ~ 2

Author(s):

Michael Shaffer ◽

Mikayla A. Borton ◽

Bridget B. McGivern ◽

Ahmed A. Zayed ◽

Sabina L. La Rosa ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Metabolic Profiling ◽

In Silico ◽

Genomic Information ◽

Human Gut ◽

Soil Community ◽

Metabolic Genes ◽

Viral Communities ◽

Specific Reactions ◽

Auxiliary Metabolic Genes

ABSTRACTMicrobial and viral communities transform the chemistry of Earth’s ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles, and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

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Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques

Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques ◽

10.47886/9781934874141.ch30 ◽

2010 ◽

Keyword(s):

Community Ecology ◽

Fish Assemblages ◽

Abiotic Factors ◽

Biotic Interactions ◽

Theoretical Models ◽

Field Studies ◽

Structure And Function ◽

Activity Levels ◽

Ecological Communities ◽

And Function

<em>Abstract</em>.—Ecological communities are structured by a combination of stochastic and deterministic processes, the latter including both abiotic factors and biotic interactions such as predation. Many studies, mostly in relatively stable ecosystems such as lakes, have demonstrated top-down effects on community structure and function. Communities or species in dynamic nonequilibrium ecosystems such as streams may also respond strongly to predation pressure. In this chapter, we review experimental research on effects of predation on fish assemblages in lotic systems, focusing on developments in the decades since Matthews and Heins (1987). Direct experimental evidence indicates that predators strongly affect lotic fish assemblages via direct and indirect pathways of lethal and nonlethal interactions. Across studies, predators consistently reduced prey density, caused changes in prey habitat use, and decreased prey activity levels. Predators may also affect aspects of prey life history and reproduction in streams, and the presence of multiple predator species may result in prey risk enhancement. Our review identified five areas needing additional research that may lead to further advances in stream fish community ecology: (1) linking predation experiments with theoretical models of fish assemblage structure and function, (2) quantifying functional traits of predators and prey, (3) manipulating whole assemblages and testing multispecies interactions, (4) understanding the role of predation in human-modified ecosystems, and (5) application of analytical approaches that facilitate integration among these areas of research as well as with observational field studies.

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Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

The ISME Journal ◽

10.1038/s41396-020-00739-3 ◽

2020 ◽

Vol 14 (12) ◽

pp. 3079-3092 ◽

Cited By ~ 2

Author(s):

Paraskevi Mara ◽

Dean Vik ◽

Maria G. Pachiadaki ◽

Elizabeth A. Suter ◽

Bonnie Poulos ◽

...

Keyword(s):

Ocean Basin ◽

Cariaco Basin ◽

Surface Ocean ◽

Metabolic Functions ◽

Metabolic Genes ◽

Water Columns ◽

Gene Vectors ◽

Viral Communities ◽

New Hosts ◽

Auxiliary Metabolic Genes

Abstract Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.

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Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest

Biochemical Journal ◽

10.1042/bcj20180482 ◽

2018 ◽

Vol 475 (19) ◽

pp. 3123-3140 ◽

Cited By ~ 5

Author(s):

Flavia Squeglia ◽

Alessia Ruggiero ◽

Rita Berisio

Keyword(s):

Stromal Cells ◽

Immune Reaction ◽

Lung Parenchyma ◽

Structure And Function ◽

Fibrillar Collagen ◽

Tissue Destruction ◽

Ecm Degradation ◽

Infected Cells ◽

Antibiotic Failure ◽

And Function

The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Nucleic Acids Research ◽

10.1093/nar/gkaa621 ◽

2020 ◽

Vol 48 (16) ◽

pp. 8883-8900 ◽

Cited By ~ 4

Author(s):

Michael Shaffer ◽

Mikayla A Borton ◽

Bridget B McGivern ◽

Ahmed A Zayed ◽

Sabina Leanti La Rosa ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Metabolic Profiling ◽

In Silico ◽

Genomic Information ◽

Human Gut ◽

Soil Community ◽

Metabolic Genes ◽

Viral Communities ◽

Specific Reactions ◽

Auxiliary Metabolic Genes

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

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Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function

10.1101/109157 ◽

2017 ◽

Author(s):

Sheila Roitman ◽

Ellen Hornung ◽

José Flores-Uribe ◽

Itai Sharon ◽

Ivo Feussner ◽

...

Keyword(s):

Fatty Acid ◽

Fatty Acid Desaturase ◽

Long Chain Fatty Acids ◽

Fatty Acid Desaturases ◽

Coping With Stress ◽

Photosynthetic Organisms ◽

Metabolic Genes ◽

Fatty Acid Profiling ◽

And Function ◽

Auxiliary Metabolic Genes

AbstractCyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host’s membrane, a fundamental stress response in living cells. We show that both viral fatty acid desaturases (vFADs) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present the first fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium to long chain fatty acids no longer than C16, in accordance to the vFADs activity. Our findings suggest that cyanophages fiddle with the infected host’s cell, leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.

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Relationship between adenovirus DNA replication proteins and nucleolar proteins B23.1 and B23.2

Journal of General Virology ◽

10.1099/vir.0.83196-0 ◽

2007 ◽

Vol 88 (12) ◽

pp. 3244-3248 ◽

Cited By ~ 22

Author(s):

Clemence E. Hindley ◽

Andrew D. Davidson ◽

David A. Matthews

Keyword(s):

Dna Replication ◽

Viral Proteins ◽

Structure And Function ◽

Replication Proteins ◽

Viral Dna ◽

Viral Dna Replication ◽

Nucleolar Structure ◽

Nucleolar Proteins ◽

Infected Cells ◽

And Function

Adenovirus infection subverts nucleolar structure and function. B23 is a nucleolar protein present in two isoforms (B23.1 and B23.2) and both isoforms have been identified as stimulatory factors for adenovirus DNA replication. Here, it is demonstrated that the two isoforms of B23, B23.1 and B23.2, interact and co-localize differently with viral DNA replication proteins pTP and DBP in adenovirus-infected cells. Thus, the mechanism by which the two proteins stimulate viral DNA replication is likely to differ. These data also demonstrate the importance of testing both isoforms of B23 for interactions with viral proteins and nucleic acids.

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