High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents

Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field

Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO₂ emission at both temperatures, and phages played a role in maintaining Q₁₀ within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased V_angle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Comprehensive analysis of waterlogging control and carbon emission reduction for optimal LID layout: a case study in campus

Nowadays, sponge city reconstruction has become the focus of research because of the increasingly serious urban waterlogging. Carbon emission reduction, waterlogging area reduction, cost, and other indicators were considered to explore the optimal sponge allocation scheme in the study area. The two-dimensional coupled model MIKE FLOOD was established to analyze the causes of waterlogging through numerical simulation. Low-impact development (LID) combination scenarios were set to analyze the control effects of waterlogging water and total runoff. The carbon emission reduction capacity and economic benefit of each scenario were calculated and evaluated. The analytic hierarchy process (AHP) was used to comprehensively evaluate the LID combination scenario and explore the optimal cost-benefit LID configuration scheme. The results show that the campus rainwater pipe network is under overload operation, and the number of overflow nodes accounts for up to 58.1% under the 3a rainfall return periods. After setting up LID measures, the runoff control rate can be increased by 26.15-42.84%, and the waterlogging area where the depth exceeds 15 cm can be reduced by 72.87-100%. If the energy conservation and emission reduction benefits and costs are considered at the same time, the layout scenario of 9% bioretention facility + 3% green roof + 3% permeable pavement can achieve the best benefits. The research can provide a reference for planning and reconstruction of sponge campus and residential areas.

Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas

Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well as in remote systems naturally enriched in HMs, such as hydrothermal vents in the deep sea. However, to date, the possible role of hydrothermal vents at shallower water depths as hot spots of microbial AR gain and spreading has not been tested, despite the higher potential risks associated with the closer vicinity of such ecosystems to coasts and human activities. In this work, we collected waters and sediments at the Panarea shallow-water hydrothermal vents, testing the presence of culturable marine bacteria and their sensitivity to antibiotics and HMs. All of the bacterial isolates showed resistance to at least one antibiotic and one HM and, most notably, 80% of them displayed multi-AR on average to 12 (min 8, max 15) different antibiotics, as well as multi-HM tolerance. We show that our isolates displayed high similarity (≥99%) to common marine bacteria, affiliating with Actinobacteria, Gammaproteobacteria, Alphaproteobacteria and Firmicutes, and all displayed wide growth ranges for temperature and salinity during in vitro physiological tests. Notably, the analysis of the genomes available in public databases for their closest relatives highlighted the lack of genes for AR, posing new questions on the origin of multi-AR acquisition in this peculiar HM-rich environment. Overall, our results point out that shallow-water hydrothermal vents may contribute to enhance AR acquisition and spreading among common marine bacteria in coastal areas, highlighting this as a focus for future research.

Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment

Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d^-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L^-1 d^-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L^-1 d^-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L^-1 d^-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.

Benthic Foraminiferal Assemblages and Rhodolith Facies Evolution in Post-LGM Sediments from the Pontine Archipelago Shelf (Central Tyrrhenian Sea, Italy)

The seabed of the Pontine Archipelago (Tyrrhenian Sea) insular shelf is peculiar as it is characterized by a mixed siliciclastic–carbonate sedimentation. In order to reconstruct the Late Quaternary paleoenvironmental evolution of the Pontine Archipelago, this study investigates the succession of facies recorded by two sediment cores. For this purpose, benthic foraminifera and rhodoliths assemblages were considered. The two cores (post-Last Glacial Maximum in age) were collected at 60 (CS1) and 122 m (Caro1) depth on the insular shelf off Ponza Island. The paleontological data were compared with seismo-stratigraphic and lithological evidence. The cores show a deepening succession, with a transition from a basal rhodolith-rich biodetritic coarse sand to the surface coralline-barren silty sand. This transition is more evident along core Caro1 (from the bottom to the top), collected at a deeper water depth than CS1. In support of this evidence, along Caro1 was recorded a fairly constant increase in the amount of planktonic foraminiferal and a marked change in benthic foraminiferal assemblages (from Asterigerinata mamilla and Lobatula lobatula assemblage to Cassidulina carinata assemblage). Interestingly, the dating of the Caro1 bottom allowed us to extend to more than 13,000 years BP the rhodolith record in the Pontine Archipelago, indicating the possible presence of an active carbonate factory at that time.

Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge

Crassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes, and 34 rRNA genes. Numerous genes are related to peptide transport, amino acid metabolism, motility, and sporulation. This agrees with the observation that strain SY095 is a spore-forming, motile, and chemoheterotrophic bacterium. Further, the genome harbors multiple prophages that carry all the genes necessary for viral particle synthesis. Some prophages carry additional genes that may be involved in the regulation of sporulation. This is the first reported genome of a bacterium from the genus Crassaminicella, providing insights into the microbial adaptation strategies to the deep-sea hydrothermal vent environment.

Drivers of Bacterial α- and β-Diversity Patterns and Functioning in Subsurface Hadal Sediments

Oceanic trenches at hadal (>6,000 m) depths are hot spots of organic matter deposition and mineralization and can host abundant and active bacterial assemblages. However, the factors able to shape their biodiversity and functioning remain largely unexplored, especially in subsurface sediments. Here, we investigated the patterns and drivers of benthic bacterial α- and β-diversity (i.e., OTU richness and turnover diversity) along the vertical profile down to 1.5 m sediment depth in the Izu-Bonin Trench (at ~10,000 m water depth). The protease and glucosidase enzymatic activity rates were also determined, as a proxy of organic matter degradation potential in the different sediment layers. Molecular fingerprinting based on automated ribosomal intergenic spacer analysis (ARISA) indicated that the α-diversity of bacterial assemblages remained high throughout the vertical profile and that the turnover (β-) diversity among sediment horizons reached values up to 90% of dissimilarity. Multivariate distance-based linear modeling (DISTLM) pointed out that the diversity and functioning of the hadal bacterial assemblages were influenced by the variability of environmental conditions (including the availability of organic resources and electron donors/acceptors) and of viral production rates along the sediment vertical profile. Based on our results, we can argue that the heterogeneity of physical-chemical features of the hadal sediments of the Izu-Bonin Trench contribute to increase the niches availability for different bacterial taxa, while viruses contribute to maintain high levels of bacterial turnover diversity and to enhance organic matter cycling in these extremely remote and isolated ecosystems.

Viral Infections Boost Prokaryotic Biomass Production and Organic C Cycling in Hadal Trench Sediments

Hadal trenches are among the most remote and least explored ecosystems on Earth and can support high benthic microbial standing stocks and activities. However, information on the role of viruses in such ecosystems and their interactions with prokaryotic hosts is very limited. Here, we investigated activities of benthic viruses and prokaryotes and their interactions in three hadal trenches (Japan, Izu-Ogasawara and Mariana trenches) and in their nearby abyssal sites. Our findings reveal that these hadal trenches, compared with the surrounding abyssal sites, support higher abundances and biomasses of prokaryotes. In addition, the high prokaryotic biomasses of hadal trenches could favor high rates of viral infection and cell lysis, especially in the Japan Trench. Hadal viruses can release large amounts of highly labile and promptly available organic material by inducing cell lysis, which could contribute to sustain benthic prokaryotes and decrease their dependency on the enzymatic digestion of the more refractory fraction of sediment organic matter. Our results suggest that this process can contribute to explain the discrepancy between high prokaryote biomass and apparent low efficiency in the utilization of the sedimentary organic matter in the hadal ecosystems. Concluding, hadal trenches may be characterized by a highly dynamic viral component, which can boost prokaryotic biomass production, thereby profoundly influencing the functioning of these remote and extreme ecosystems.

Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters

Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under lysogen-induced and non-induced treatments. The lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Alteromonadaceae, and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.

Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis

Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome.

Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton

Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify.

High Incidence of Lysogeny in the Oxygen Minimum Zones of the Arabian Sea (Southwest Coast of India)

Though microbial processes in the oxygen minimum zones (OMZs) of the Arabian Sea (AS) are well documented, prokaryote-virus interactions are less known. The present study was carried out to determine the potential physico-chemical factors influencing viral abundances and their life strategies (lytic and lysogenic) along the vertical gradient in the OMZ of the AS (southwest coast of India). Water samples were collected during the southwest monsoon (SWM) season in two consecutive years (2015 and 2016) from different depths, namely, the surface layer, secondary chlorophyll a maxima (~30–40 m), oxycline (~70–80 m), and hypoxic/suboxic layers (~200–350 m). The high viral abundances observed in oxygenated surface waters (mean ± SD = 6.1 ± 3.4 × 10⁶ viral-like particles (VLPs) mL⁻¹), drastically decreased with depth in the oxycline region (1.2 ± 0.5 × 10⁶ VLPs mL⁻¹) and hypoxic/suboxic waters (0.3 ± 0.3 × 10⁶ VLPs mL⁻¹). Virus to prokaryote ratio fluctuated in the mixed layer (~10) and declined significantly (p < 0.001) to 1 in the hypoxic layer. Viral production (VP) and frequency of virus infected cells (FIC) were maximum in the surface and minimum in the oxycline layer, whereas the viral lysis was undetectable in the suboxic/hypoxic layer. The detection of a high percentage of lysogeny in suboxic (48%) and oxycline zones (9–24%), accompanied by undetectable rates of lytic viral infection support the hypothesis that lysogeny may represent the major survival strategy for viruses in unproductive or harsh nutrient/host conditions in deoxygenated waters.

Potential impact of global climate change on benthic deep-sea microbes

Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.