Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.CAPESCNPqFAPERJCiencia sem fronteiras programUniv Fed Rio de Janeiro, IB, BR-21944970 Rio de Janeiro, BrazilRadboud Univ Nijmegen, Radboud Inst Mol Life Sci, CMBI, Med Ctr, NL-6500 HB Nijmegen, NetherlandsUniv Utrecht, Theoret Biol & Bioinformat, NL-3584 CH Utrecht, NetherlandsSan Diego State Univ, Dept Biol, San Diego, CA 92182 USAUniv Fed Sao Paulo UNIFESP, Dept Ciencias Mar, BR-11070100 Baixada Santista, BrazilNIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, POB 59, NL-1790 AB Den Burg, NetherlandsUniv Utrecht, POB 59, NL-1790 AB Den Burg, NetherlandsUniv Amsterdam, Dept Aquat Microbiol, IBED, NL-1090 GE Amsterdam, NetherlandsUniv Fed Rio de Janeiro, COPPE, SAGE, BR-21941950 Rio de Janeiro, BrazilUniv Fed Sao Paulo UNIFESP, Dept Ciencias Mar, BR-11070100 Baixada Santista, BrazilCAPESCNPqFAPERJCiencia sem fronteiras program: 864.14.004Web of Scienc

Metagenomics in Polluted Aquatic Environments

Metagenomics is defined as the culture-independent genomic analysis of biological assemblages providing access to the whole set of genes and genomes from a sample. It encompasses a variety of techniques that are based on (i) total DNA extraction from samples followed by PCR amplification of specific genes, (ii) library construction or amplification and sequencing of the whole genetic material. These methodologies have successfully been applied in studies of composition, dynamics, and functions of microbial communities in a variety of ecosystems including those subjected to anthropogenic modifications (Gilbert & Dupont, 2011). Culture independent methods allow the analysis of a set of metabolic genes from microbial communities, which can be used to determine how environmental conditions such as pollution can shape community composition and the diversity of genes associated with biogeochemical cycles such as those of carbon, nitrogen, and phosphorus (Singh et al., 2009). This approach is also useful for the discovery of novel environmental microorganisms and genes, with important applications for biotechnology, medicine, and bioremediation (Cardoso et al., 2011). This applicability has resulted in a recent sharp increase in studies focusing in the metagenomic analysis of polluted sites. Their aim is to characterize microbial communities from a diverse set of environments such as freshwater, marine sediments, open ocean, pelagic ecosystems, soil, and host-associated communities. An example of these initiatives is the Global Ocean Sampling Expedition (GOS), which assessed the genetic diversity of marine microbial communities around the Earth. Since 2003, an enormous amount of data has been generated by GOS helping scientists to reveal the microbial diversity and also allowing them to better understand microbial phylogeny and ecology (Gilbert & Dupont, 2011)

Extending the natural adaptive capacity of coral holobionts

Anthropogenic climate change and environmental degradation destroy coral reefs, the ecosystem services they provide, and the livelihoods of close to a billion people who depend on these services. Restoration approaches to increase the resilience of corals are therefore necessary to counter environmental pressures relevant to climate change projections. In this Review, we examine the natural processes that can increase the adaptive capacity of coral holobionts, with the aim of preserving ecosystem functioning under future ocean conditions. Current approaches that centre around restoring reef cover can be integrated with emerging approaches to enhance coral stress resilience and, thereby, allow reefs to regrow under a new set of environmental conditions. Emerging approaches such as standardized acute thermal stress assays, selective sexual propagation, coral probiotics, and environmental hardening could be feasible and scalable in the real world. However, they must follow decision-making criteria that consider the different reef, environmental, and ecological conditions. The implementation of adaptive interventions tailored around nature-based solutions will require standardized frameworks, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination

Benthic assemblages are more predictable than fish assemblages at an island scale

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sandin, S. A., Alcantar, E., Clark, R., de Leon, R., Dilrosun, F., Edwards, C. B., Estep, A. J., Eynaud, Y., French, B. J., Fox, M. D., Grenda, D., Hamilton, S. L., Kramp, H., Marhaver, K. L., Miller, S. D., Roach, T. N. F., Seferina, G., Silveira, C. B., Smith, J. E., Zgliczynski, B. J., & Vermeij, M. J. A. Benthic assemblages are more predictable than fish assemblages at an island scale. Coral Reefs, 41, (2022.): 1031–1043, https://doi.org/10.1007/s00338-022-02272-5.Decades of research have revealed relationships between the abundance of coral reef taxa and local conditions, especially at small scales. However, a rigorous test of covariation requires a robust dataset collected across wide environmental or experimental gradients. Here, we surveyed spatial variability in the densities of major coral reef functional groups at 122 sites along a 70 km expanse of the leeward, forereef habitat of Curaçao in the southern Caribbean. These data were used to test the degree to which spatial variability in community composition could be predicted based on assumed functional relationships and site-specific anthropogenic, physical, and ecological conditions. In general, models revealed less power to describe the spatial variability of fish biomass than cover of reef builders (R2 of best-fit models: 0.25 [fish] and 0.64 [reef builders]). The variability in total benthic cover of reef builders was best described by physical (wave exposure and reef relief) and ecological (turf algal height and coral recruit density) predictors. No metric of anthropogenic pressure was related to spatial variation in reef builder cover. In contrast, total fish biomass showed a consistent (albeit weak) association with anthropogenic predictors (fishing and diving pressure). As is typical of most environmental gradients, the spatial patterns of both fish biomass density and reef builder cover were spatially autocorrelated. Residuals from the best-fit model for fish biomass retained a signature of spatial autocorrelation while the best-fit model for reef builder cover removed spatial autocorrelation, thus reinforcing our finding that environmental predictors were better able to describe the spatial variability of reef builders than that of fish biomass. As we seek to understand spatial variability of coral reef communities at the scale of most management units (i.e., at kilometer- to island-scales), distinct and scale-dependent perspectives will be needed when considering different functional groups.This research and the larger efforts of Blue Halo Curacao were supported by funding from the Waitt Institute and with permissions from the Government of Curacao, Ministry of Health, Environment, and Nature. Field logistics were further supported by the Waitt Institute vessel crew, CARMABI Foundation, The Dive Shop Curacao, and Dive Charter Curacao

Environmental Shaping of Sponge Associated Archaeal Communities

Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments

Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome

Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient’s lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient’s strain was resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions