Virus-host systems in sea ice

Virus-host systems in sea ice Sea ice is one of the largest habitats on Earth. A specialized microbial community lives inside the narrow brine channels that are formed during freezing process, when salt and other components from sea water concentrate between ice crystals. These microbes have an active role in the biogeochemistry of the sea ice by primary production, degradation of material and excreation of compounds, which effect the gas exchange between the ocean and atmosphere and the nutrient status of the under ice sea. Sea ice microbial community consist of auto- and heterotrophic protists, prokaryotes and viruses. The main heterotrophs are the bacteria. Viruses are the most abundant lifeform on Earth. They are found everywhere where there is life and they infect all kinds of cells. Infections are crucial for viruses because they can reproduce only by using a host cell to produce new virus particles. Majority of the viruses infect the most numerous cells on Earth, the prokaryotes, i.e. bacteria and archaea. Viruses infecting bacteria (bacteriophages or phages) are a major factor in bacterial mortality. They can also control the community composition of bacteria because of the high specificity of the infection. Bacteria have different mechanisms to avoid phage infections and phages need to evolve to be able to reproduce. This arms race of phages and bacteria can lead to co-evolution. Although viruses are known to have significant effects on bacterial communities in various habitats, not much is known about the viruses in the sea ice. Before this project, only three isolates have been reported from the Arctic sea ice. The aim in this thesis was to get a better understanding of the phages and their role in sea ice. For that, isolation, cultivation and purification methods needed to be developed and optimized. Bacteria and phages were isolated from samples taken from Baltic and Antarctic sea ice. The phage particles were purified and characterized by their morphology, structural protein patterns and host range. The identities of the host bacteria were analyzed by their 16S rRNA gene sequence. Effect of temperature on the host bacterial growth and phage infections, and the adsorption and life cycle of the phages, was experimentally studied. The abundance of virus-like particles in Antarctic sea ice was analyzed using flow cytometry. The first phage-host systems were isolated from Baltic Sea ice and Antarctic sea ice. All of the phages infected bacterial strains belonging to genera that are typically abundant in sea ice i.e. Shewanella, Flavobacterium, Paraglaciecola and Octadecabacter. All the bacterial strains and phages were cold-active. The adsorption and life cycle of phages was suprisingly fast at tested 4 °C. The phage infections were specific to certain bacterial strains. A complex phage-host system network was seen among two of the phages and 15 closely related bacterial strains from Antarctica, which may be a result of co-evolution. The abundance of virus-like particles in melted Antarctic winter sea ice (105 106 particles ml-1 bulk ice) was high when considering that they are normally concentrated in the brine channels. The amount of virus-like particles in sea ice even during Antarctic winter, indicates that viruses are an active and important member of the sea ice microbial community. Adsorption and life cycle studies show that phage infections may be efficient in the closed and concentrated environment of sea ice brines. By the strain specificic infections the phages can control the bacterial community composition and this way effect the community functions. The co-evolution of phages and bacteria may be important factor in the bacterial evolution.Virukset ja niiden isäntäbakteerit merijäässä Merijää on yksi maapallon suurimmista elinalueista. Erityinen mikrobiyhteisö elää merijään sisällä olevissa suolavesikanavissa, jotka muodostuvat meriveden jäätyessä, kun suola ja muut epäpuhtaudet tiivistyvät jääkiteiden väliin. Nämä mikrobit muokkaavat merijään rakennetta ja kemiallista koostumusta yhteyttämällä, ja hajottamalla sekä erittämällä yhdisteitä. Tämä vaikuttaa mm. kaasujen vaihtoon meren ja ilmakehän välillä ja merijään alapuolisen veden ravinnetilanteeseen. Merijään mikrobiyhteisö koostuu alkueliöistä ja alkeistumallisista sekä viruksista. Virukset ovat maapallon yleisin elämänmuoto ja niitä löytyy kaikkialta. Virukset lisääntyvät infektoimalla solullisia eliöitä ja tuottamalla uusia viruskappaleita näiden avulla. Valtaosa viruksista infektoi maapallon yleisimpiä solullisia eliöitä, alkeistumallisia bakteereita ja arkeoneja. Bakteereita infektoivat virukset (bakteriofagit tai faagit) ovat merkittävä syy bakteerien kuolleisuuteen ja mahdollisesti myös evoluutioon. Vaikka tiedetään, että yleisesti virusten merkitys bakteeriyhteisöihin on merkittävä, merijään viruksista on vain hyvin vähän tutkittua tietoa. Ennen tätä tutkimusta merijäästä on eristetty vain kolme faagia Pohjoiselta jäämereltä. Tämän tutkimuksen tarkoituksena oli selvittää faagien merkitystä merijäässä eristämällä niitä ja niiden isäntäbakteereita tarkempia tutkimuksia varten Itämerestä ja Etelämannerta ympäröivästä Eteläisestä jäämerestä. Jotta tämä oli mahdollista, oli kehitettävä ja paranneltava eristys-, kasvatus- ja puhdistusmenetelmiä. Eristettyjen faagien ulkomuoto määritettiin ja niiden rakenneproteiineja vertailtiin keskenään, jotta voitiin varmistaa faagien olevan keskenään erilaisia. Isäntäbakteerien suku määritettiin. Tutkittiin lämpötilan vaikutusta bakteerien kasvuun ja faagien infektioon, kuten myös faagien tarttumista isäntäsolun pintaan ja uusien fagipartikkelien tuotannon kestoa. Myös viruksen kaltaisten kappaleiden määrää mitattiin Eteläisen jäämeren merijäästä virtaussolulaskennan avulla. Tämän tutkimuksen aikana eristettiin ensimmäiset faagit isäntäbakteereineen Itämeren ja Eteläisen jäämeren merijäästä. Kaikki eristetyistä faageista infektoivat bakteerikantoja, jotka kuuluvat yleisiin merijäästä löydettyihin bakteerisukuihin Shewanella, Flavobacterium, Paraglaciecola ja Octadecabacter. Kukin faagi pystyi infektoimaan vain tiettyjä bakteerikantoja. Kaikki bakteerikannat ja faagit olivat sopeutuneita kylmiin olosuhteisiin. Faagin tarttuminen isäntäsolun pintaan ja uusien viruspartikkelien tuotanto tapahtuivat yllättävän nopeasti kylmissä olosuhteissa. Kaksi faageista infektoi eri tehokkuuksilla 15 läheisesti sukua olevaa bakteerikantaa, mikä saattaa johtua faagien ja bakteerien keskinäisestä sodankäynnistä ja evoluutiosta. Viruksen kaltaisia kappaleita oli Eteläiseltä jäämereltä otetuissa näytteissä 105 106 kappaletta millilitrassa sulatettua merijäätä. Tämä on runsas määrä, erityisesti kun jäävirukset ovat normaalisti tiivistettynä kapeisiin suolavesikanaviin. Virusten kaltaisten kappaleiden suuri määrä Eteläisen jäämeren merijäässä osoittaa, että virukset ovat tärkeä osa jäämikrobiyhteisöä. Jäävirusinfektiot vaikuttavat myös olevan hyvin tehokkaita, sillä ne kykenevät tarttumaan isäntäsoluun ja lisääntymään nopeasti. Infektoimalla vain tiettyjä, tarkasti määrättyjä bakteerikantoja, virukset voivat muokata bakteeriyhteisön lajisuhteita ja vaikuttaa näin yhteisön toimintaan. Virusten ja bakteerien välinen sodankäynti voi olla tärkeä tekijä bakteerien evoluutiossa

Autumn to spring microbial community in the northern Baltic Sea : temporal variability in bacterial, viral and nanoflagellate abundance during the cold-water season

Marine microbial communities undergo drastic changes during the seasonal cycle in high latitude seas. Despite the dominance of microbial biomass in the oceans, comprehensive studies on the seasonal changes of microbial plankton during the complete winter period are lacking. To study the seasonal variation in abundance of the microbial community, water samples were collected weekly in the Northern Baltic Sea from October to May. During ice cover from mid-January to April, samples from the sea ice and the underlying water were taken in addition to the water column samples. Abundances of bacteria, virus-like particles, nanoflagellates, and chlorophyll a concentrations were measured from sea ice, under-ice water, and the water column, and examined in relation to environmental conditions. All studied organisms had clear seasonal changes in abundance, and the sea-ice microbial community had an independent wintertime development compared to the water column. Bacteria were observed to have a key role in the biotic interactions in both ice and the water column, and the dormant period during the cold-water months (October–May) was limited to before ice formation. Our results provide the first insights into the temporal dynamics of bacteria and viruses during the whole cold-water season (October–May) in coastal high latitude seas, and demonstrate that changes in the environmental conditions are likely to affect bacterial dynamics and have implications on trophic interactions

The first known virus isolates from Antarctic sea ice have complex infection patterns

Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0 degrees C and 4 degrees C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.Peer reviewe

Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature

Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, Halomonas sp. 363 and Paracoccus sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4 degrees C when the availability of nitrogen and/or oxygen limited growth. The genome of Halomonas sp. 363 carries three phaC synthase genes and transcribes genes along three PHA pathways (I to III), whereas Paracoccus sp. 392 carries only one phaC gene and transcribes genes along one pathway (I). Thus, Halomonas sp. 363 has a versatile repertoire of phaC genes and pathways enabling production of both short- and medium-chain-length PHA products. IMPORTANCE Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, Halomonas sp. 363 and Paracoccus sp. 392, are able to produce various types of PHA from inexpensive carbon sources. Halomonas sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.peerReviewe

Virus-host interactions and genetic diversity of Antarctic Sea Ice bacteriophages

ABSTRACT Although we know the generally appreciated significant roles of microbes in sea ice and polar waters, detailed studies of virus-host systems from such environments have been so far limited by only a few available isolates. Here, we investigated infectivity under various conditions, infection cycles, and genetic diversity of the following Antarctic sea ice bacteriophages: Paraglaciecola Antarctic GD virus 1 (PANV1), Paraglaciecola Antarctic JLT virus 2 (PANV2), Octadecabacter Antarctic BD virus 1 (OANV1), and Octadecabacter Antarctic DB virus 2 (OANV2). The phages infect common sea ice bacteria belonging to the genera Paraglaciecola or Octadecabacter. Although the phages are marine and cold-active, replicating at 0°C to 5°C, they all survived temporal incubations at ≥30°C and remained infectious without any salts or supplemented only with magnesium, suggesting a robust virion assembly maintaining integrity under a wide range of conditions. Host recognition in the cold proved to be effective, and the release of progeny viruses occurred as a result of cell lysis. The analysis of viral genome sequences showed that nearly one-half of the gene products of each virus are unique, highlighting that sea ice harbors unexplored virus diversity. Based on predicted genes typical for tailed double-stranded DNA phages, we suggest placing the four studied viruses in the class Caudoviricetes. Searching against viral sequences from metagenomic assemblies, we revealed that related viruses are not restricted to Antarctica but are also found in distant marine environments. IMPORTANCE Very little is known about sea ice microbes despite the significant role played by sea ice in the global oceans as well as microbial input into biogeochemical cycling. Studies on the sea ice viruses have been typically limited to -omics-based approaches and microscopic examinations of sea ice samples. To date, only four cultivable viruses have been isolated from Antarctic sea ice. Our study of these unique isolates advances the understanding of the genetic diversity of viruses in sea ice environments, their interactions with host microbes, and possible links to other biomes. Such information contributes to more accurate future sea ice biogeochemical models

Physical and bacterial controls on inorganic nutrients and dissolved organic carbon during a sea ice growth and decay experiment

We investigated how physical incorporation, brine dynamics and bacterial activity regulate the distribution of inorganic nutrients and dissolved organic carbon (DOC) in artificial sea ice during a 19-day experiment that included periods of both ice growth and decay. The experiment was performed using two series of mesocosms: the first consisted of seawater and the second consisted of seawater enriched with humic-rich river water. We grew ice by freezing the water at an air temperature of -14 °C for 14 days after which ice decay was induced by increasing the air temperature to -1 °C. Using the ice temperatures and bulk ice salinities, we derived the brine volume fractions, brine salinities and Rayleigh numbers. The temporal evolution of these physical parameters indicate that there was a succession of 3 stages in the brine dynamics: forced-convection, followed by bottom convection during ice growth, and then brine stratification during ice decay. The major findings are: (1) the incorporation of dissolved compounds (nitrate, nitrite, ammonium, phosphate, silicate, and DOC) into the sea ice was not conservative (relative to salinity) during ice growth. Brine convection clearly influenced the incorporation of the dissolved compounds, since the non-conservative behavior of the dissolved compounds was particularly pronounced in the absence of brine convection. (2) Bacterial activity further regulated nutrient availability in the ice: ammonium and nitrite accumulated as a result of remineralization processes, although bacterial production was too low to induce major changes in DOC concentrations. (3) Different forms of DOC have different properties and hence incorporation efficiencies. In particular, the terrestrially-derived DOC from the river water was less efficiently incorporated into sea ice than the DOC in the seawater. Therefore the main factors regulating the distribution of the dissolved compounds within sea ice are clearly a complex interaction of brine dynamics, biological activity and in the case of dissolved organic matter, the physico-chemical properties of the dissolved constituents themselves

Usuing the Arctic Environment Test Basin to study the dynamics of dissolved organic matter in sea ice

This is a report from the INTERICE 5 project that used the Arctic Environment Test Basin at HSVA from 21 May to 19 June 2012. The overarching aim was to investigate the physical and biological controls of dissolved organic matter incorporation into growing sea ice and the effect of melting once the ice had consolidated. Measurements were also made on the CO2 fluxes at the ice surface in relation to the chemical and biological changes taking place in the ice. The Interice 5 team was a multidisciplinary group of glaciologists, chemists and microbiologists from Belgium, Denmark, Finland, Germany and U.K. They were able to build on the experiences of previous INTERICE 2, 3 & 4 projects to maximize the opportunities from the facility. The preliminary results from the experiment will be presented, in the context of what is known about these processes from field campaigns

An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community

peer reviewedAntarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to high (o4 μg l–1) chlorophyll-a (chl-a) concentrations and consequent bacterial production. Typical sea-ice bacterial genera, for example, Octadecabacter, Polaribacter and Glaciecola, often abundant in spring and summer during the sea-ice algal bloom, predominated in the communities. The variability in bacterial community composition in the different ice types was mainly explained by the chl-a concentrations, suggesting that as in spring and summer sea ice, the sea-ice bacteria and algae may also be coupled during the Antarctic winter. Coupling between the bacterial community and sea-ice algae was further supported by significant correlations between bacterial abundance and production with chl-a. In addition, sulphate-reducing bacteria (for example, Desulforhopalus) together with odour of H2S were observed in thick, apparently anoxic ice, suggesting that the development of the anaerobic bacterial community may occur in sea ice under suitable conditions. In all, the results show that bacterial community in Antarctic sea ice can stay active throughout the winter period and thus possible future warming of sea ice and consequent increase in bacterial production may lead to changes in bacteria-mediated processes in the Antarctic sea-ice zone