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

Mara, Paraskevi; Vik, Dean; Pachiadaki, Maria; Suter, Elizabeth A.; Poulos, Bonnie T.; Taylor, Gordon T.; Edgcomb, Virginia P.

doi:10.1038/s41396-020-00739-3

Cited by 43 publications

(45 citation statements)

References 98 publications

(138 reference statements)

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“…The present study, together with others from the Black Sea [5,9] (bioproject PRJNA649215) and the Cariaco Basin in Venezuela [10,11] provide a first glimpse into the microbiome of anoxic marine water columns and Oxygen Minimum Zones (OMZs). The redoxclines of these habitats show a convergence of various coexisting metabolisms, among which we encounter anoxygenic photosynthesis such as that one observed in Chlorobium phaeobacteroides [27], ammonia oxidation by Nitrosopumilus spp., chemolithotrophic metabolisms carried by Gammaproteobacteria such Ca.…”

Section: Discussionmentioning

confidence: 82%

“…To assess the representativity of our samples we compared the community structure by 16S rRNA gene (following the same abovementioned methodology) and the read similarity (clustering) among various similar datasets, including other Black Sea metagenomes available (PRJNA649215) [9] (see Fig. S1) and with a former sampling campaign from another marine euxinic system, the Cariaco Basin [10,11] (see Fig. S2).…”

Section: Comparison Of the Black Sea And Cariaco Basin Metagenomic Damentioning

confidence: 99%

“…Another habitat that could be comparable to the Black Sea in terms of water column stratification is the Cariaco Basin (Venezuela). Several studies on the redoxcline and euxinic strata on this system provided some of the first insights into microbial structuring in anoxic marine waters and Oxygen Minimum Zones (OMZs) [10,11].…”

Section: Introductionmentioning

confidence: 99%

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The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2021

Environmental Microbiome

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Background The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

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Section: Discussionmentioning

confidence: 82%

Section: Comparison Of the Black Sea And Cariaco Basin Metagenomic Damentioning

confidence: 99%

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The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2021

Environmental Microbiome

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“…Based on the evidence of unique SSF proteins found in three distinct viral genomes and the phylogenetic divergence from host proteins, the likelihood that they are randomly packaged host genes is low. Although the function of the viral SSF proteins requires experimental confirmation, we suspect this relatively large gene (mean protein length 1265 amino acidss) to be beneficial for the viral populations, as it was identified in multiple viruses despite the presumed high cost of maintenance of AMGs in viral genomes (51,52).…”

Section: Sequence-informed Putative Host-virus Interactions Indicate Dispersal Of Hosts And/or Virusesmentioning

confidence: 99%

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

Hwang

Rahlff

Schulze‐Makuch

et al. 2020

Preprint

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Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show dispersal of diverse and abundant viruses that infect a wide range of hosts over 205 km across the desert. Host genomes encoded both adaptive and innate immune systems, providing evidence of viral predation being a key selective pressure along with abiotic stresses. Viral genomes carried extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage) and other auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.ImportanceDeserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that viruses are abundant, diverse and widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex evolutionary dynamics that shape the unique and poorly understood host-virus relationships in desert soils.

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“…Bacteriophages can affect the diversity and function of aquatic microbial populations through the incorporation and expression of auxiliary metabolic genes (AMGs). Currently, phage-encoded AMGs are reported to include multiple types of genes involved in not only main nutrient cycle pathways, such as carbon metabolism [12][13][14], nitrogen [15], phosphorus [16] and sulfur cycling [17,18], but also some speci c pathways, such as acetate fermentation [19], methane oxidation [14], nucleotide metabolism [20] and oxidative stress responses [21]. Taken together, these ndings imply that viral AMGs in uence most, if not all, pathways of microbial metabolism.…”

Section: Introductionmentioning

confidence: 99%

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

Tao¹,

Gao²,

Li³

et al. 2020

Preprint

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Background: In aquatic ecosystems, bacteriophages play key roles in species diversity, host population dynamics and functional gene transfer. Due to a lack of high-throughput experimental tools to obtain robust associations between bacteriophages and hosts, the current metagenome-based phage community research generally predicts interactions based on various computational pipelines. In this study, by introducing an in vivo proximity-ligation chromosomal confirmation capture (Hi-C) technique combined with existing sequencing data from a freshwater metagenome study, we investigated double-stranded DNA (dsDNA) bacteriophages distribution, bacteriophage-host associations and abundance profiles at various depths in a deep alpine lake.Results: A total of 985 nonredundant viral genomes (containing 1,464 viral contigs measuring at least 10 kb) were identified using rigorous bioinformatic pipelines, and 67.3% of bacteriophages had never been reported previously. The bacteriophages had a significant depth-dependent distribution, and 56.9% of phage populations were only present in the epilimnion. Overall, 567 auxiliary metabolic genes (AMGs) were identified in 239 phages (24.26% of the total population). Hi-C reconstructed 58 bacteriophage-host association events encompassing eight bacterial phyla, among which 14 AMG-coding bacteriophages were clearly linked to their hosts. Three bacteriophages contained the mec gene, which was exactly complementary to their hosts in the sulfur-related pathway, and three other bacteriophages contained AMGs that likely participated in host fructose and mannose metabolism.Conclusions: The present study identifies bacteriophages in Lake Fuxian and describes the bacteriophages and their host dynamics along the depth profile. Our results indicate that metagenomics combined with the Hi-C technique has promise for future applications in high-throughput bacteriophage identification and bacteriophage-host association detection, which could further extend our knowledge of the functional roles played by bacteriophages in aquatic ecosystems.

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

Cited by 43 publications

References 98 publications

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

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