Ice formation, growth and associated substrate supply determine sea-ice bacterial community dynamics

Sea ice, at its maximum extent, is one of the largest biomes on Earth. In addition to the polar oceans, it covers extensive sea areas at lower latitudes such as the Baltic Sea and the Sea of Okhotsk. During ice formation, organic and inorganic components in the parent seawater are concentrated into saline brines within the ice, which serve as a habitat for diverse auto- and heterotrophic organisms, including bacteria. Sea-ice bacteria are responsible for many biogeochemical processes, such as decomposition of particulate organic matter, recycling of dissolved organic matter and remineralization of nutrients, analogously to bacterially driven biogeochemical processes in the water column. Since bacterial groups vary by their metabolic traits and participation in biogeochemical processes, knowledge of the bacterial community structure and its seasonal variation is essential for an understanding of ice biogeochemistry. This thesis characterises sea-ice bacterial communities during ice formation and during the winter/spring transition phase when the community composition is poorly known. Bacterial communities in Arctic and Baltic sea ice during the winter/spring transition were studied and compared. In addition, the effect of the dissolved organic matter regime on bacterial community formation was investigated in an experimental sea-ice system with North Sea water. The main methods applied were terminal-restriction fragment length polymorphism and/or Illumina Miseq sequencing together with bacterial production and abundance measurements. During the early stages of sea-ice formation, the bacterial communities were similar to the parent water communities, suggesting that the parent water determines the initial sea-ice bacterial community composition. After congealment of the sea ice, the bacterial communities changed towards communities typical of sea ice in spring. During the winter/spring transition, members of the classes Flavobacteriia (formerly Flavobacteria), Gammaproteobacteria and Alphaproteobacteria were predominant both in Baltic and Arctic sea ice. The Baltic and Arctic sea-ice bacterial communities were significantly different; however, a few members of common sea-ice bacterial genera, such as Polaribacter and Shewanella, were closely related, pointing to similar selection in ice, regardless of differences in the prevailing environmental conditions. In the experimental system, the bacterial communities were able to respond to altered substrate availability immediately after ice formation. This indicates successful adaptation of sea-ice bacteria to major shifts in temperature and salinity during ice formation. The results of this thesis suggest that sea-ice bacterial community formation and dynamics is defined by a combination of changes in environmental conditions during sea-ice maturation and its associated substrate availability, as well as resource competition. The sea-ice habitat provides an example of the enormous capacity of bacteria to adapt to changing environments and how minor members of the bacterial community can become predominant when environmental conditions change.Merijää peittää vuosittain jopa 7% maapallon pinta-alasta muodostaen yhden maapallon suurimmista eloyhteisöistä eli biomeista. Napa-alueiden lisäksi merijäätä muodostuu vuotuisesti myös alempien leveysasteiden merialueilla, kuten Itämerellä ja Ohotanmerellä. Merijään muodostuessa, meriveteen liuenneet orgaaniset ja epäorgaaniset ainesosat väkevöityvät toisiinsa takertuneiden jääkiteiden väliin muodostaen jään sisälle pieniä suolavesikanavia ja taskuja. Suolavesikanavissa ja taskuissa elää mikroskooppisia pieneliöitä, kuten bakteereita. Merijään bakteerit osallistuvat moniin biogeokemiallisiin prosesseihin kuten partikkelimaisen orgaanisen aineksen hajotukseen sekä liuenneen orgaanisen aineksen että ravinteiden kierrätykseen samaan tapaan kuin jään alla olevassa vesipatsaassa. Bakteeriyhteisöt koostuvat erilaisten bakteerilajien populaatioista joilla kullakin on oma tehtävänsä biogeokemiallisissa kierroissa. Jotta voisimme ymmärtää eri bakteeritaksonien tehtävät merijään biogeokemiallisissa kierroissa, on selvitettävä kuinka bakteeriyhteisöt muodostuvat ja kuinka ne muuttuvat vuodenaikojen mukaan. Väitöskirjatyöni tarkoituksena oli kartoittaa bakteeriyhteisöjen rakennetta ja dynamiikkaa sekä merijään muodostuessa että kevättalvella, jolloin bakteeriyhteisön rakenne on puutteellisesti tunnettu. Näytteitä kerättiin sekä Itämereltä että Pohjoiselta jäämereltä. Bakteeriyhteisöjä tutkittiin myös kokeellisessa tutkimuksessa, jossa selvitettiin liuenneen orgaanisen aineksen laadun ja määrän vaikutusta muodostuviin bakteeriyhteisöihin. Bakteeriyhteisöjen rakennetta tutkittiin 16S rRNA geenin päätekatkokirjoanalyysillä ja DNA-jaksotuksella sekä vakiintunutta Sangerin jaksotusmenetelmää että syväjaksotusta käyttäen. Lisäksi bakteeriyhteisöjen runsautta ja aktiivisuutta tutkittiin bakteeribiomassa- ja bakteerituotantomittauksilla. Jään muodostuessa bakteeriyhteisöt olivat hyvin samankaltaisia kuin vedessä mikä viittaa lähtöveden bakteeriyhteisön määräävän jään bakteeriyhteisön koostumuksen jäätymisen alkaessa. Jääpeitteen vahvistuessa yhteisöt erilaistuivat vesiyhteisöistä ja alkoivat muistuttaa rakenteeltaan kevätjäälle tyypillisiä yhteisöjä. Sekä Itämerellä että Pohjoisella jäämerellä yhteisöissä esiintyi runsaimmin Flavobacteriia (aikaisemmin Flavobacteria), Gammaproteobacteria and Alphaproteobacteria luokkien bakteereita. Kokonaisuudessaan Itämeren ja Pohjoisen jäämeren yhteisöt olivat erilaisia, mutta yhteisöistä havaittiin myös muutamia bakteerisukuja kuten Polaribacter ja Shewanella, joiden 16S rRNA geeniä koodaavat DNA-jaksot olivat keskenään hyvin samankaltaisia (>97%). Geenien samankaltaisuus viittaa samankaltaisiin valintapaineisiin huolimatta Itämeren ja Pohjoisen jäämeren erilaisista ympäristöolosuhteista. Bakteeriyhteisöt muuttuivat kokeellisissa olosuhteissa hyvin nopeasti jäätymisen alettua kun veteen lisättiin liuennutta orgaanista ainesta. Tulos viittaa bakteerien kykyyn sopeutua nopeasti muuttuvaan suolaisuuteen ja lämpötilaan. Väitöskirjani tulosten perusteella merijään bakteeriyhteisöjen muodostumiseen ja dynamiikkaan vaikuttavat ympäristöolosuhteiden muutos jään muodostuessa ja kasvaessa, tarjolla olevan substraatin saatavuus sekä bakteerien välinen kilpailu. Merijään bakteeriyhteisöjen muodostuminen on esimerkki bakteerien huomattavasta kyvystä sopeutua muuttuviin ympäristöolosuhteisiin sekä ympäristöolosuhteiden muutoksen nopeasta heijastumisesta bakteeriyhteisöjen rakenteeseen

Contrasting patterns of carbon cycling and dissolved organic matter processing in two phytoplankton-bacteria communities

Microbial consumption of phytoplankton-derived organic carbon in the pelagic food web is an important component of the global C cycle. We studied C cycling in two phytoplankton-bacteria systems (non-axenic cultures of a dinoflagellate Apocalathium malmogiense and a cryptophyte Rhodomonas marina) in two complementary experiments. In the first experiment we grew phytoplankton and bacteria in nutrient-replete conditions and followed C processing at early exponential growth phase and twice later when the community had grown denser. Cell-specific primary production and total community respiration were up to 4 and 7 times higher, respectively, in the A. malmogiense treatments. Based on the optical signals, accumulating dissolved organic C (DOC) was degraded more in the R. marina treatments, and the rate of bacterial production to primary production was higher. Thus, the flow of C from phytoplankton to bacteria was relatively higher in R. marina treatments than in A. malmogiense treatments, which was further supported by faster C-14 transfer from phytoplankton to bacterial biomass. In the second experiment we investigated consumption of the phytoplankton-derived DOC by bacteria. DOC consumption and transformation, bacterial production, and bacterial respiration were all higher in R. marina treatments. In both experiments A. malmogiense supported a bacterial community predominated by bacteria specialized in the utilization of less labile DOC (class Bacteroidia), whereas R. marina supported a community predominated by copiotrophic Alphaand Gammaproteobacteria. Our findings suggest that large dinoflagellates cycle relatively more C between phytoplankton biomass and the inorganic C pool, whereas small cryptophytes direct relatively more C to the microbial loop.Peer reviewe

Polycyclic aromatic hydrocarbon sorption and bacterial community composition of biodegradable and conventional plastics incubated in coastal sediments

Resistant to degradation, plastic litter poses a long-term threat to marine ecosystems. Biodegradable materials have been developed to replace conventional plastics, but little is known of their impacts and degradation in marine environments. A 14-week laboratory experiment was conducted to investigate the sorption of polycyclic aromatic hydrocarbons (PAHs) to conventional (polystyrene PS and polyamide PA) and bio-based, biodegradable plastic films (cellulose acetate CA and poly-L-lactic acid PLLA), and to examine the composition of bacterial communities colonizing these materials. Mesoplastics (1 cm(2)) of these materials were incubated in sediment and seawater collected from two sites in the Gulf of Finland, on the coast of the highly urbanized area of Helsinki, Finland. PS sorbed more PAHs than did the other plastic types at both sites, and the concentration of PAHs was consistently and considerably smaller in plastics than in the sediment. In general, the plastic bacterial biofilms resembled those in the surrounding media (water and/or sediment). However, in the sediment incubations, the community composition on CA diverged from that of the other three plastic types and was enriched with Bacteroidia and potentially cellulolytic Spirochaetia at both sites. The results indicate that certain biodegradable plastics, such as CA, may harbour potential bioplastic-degrading communities and that PAH sorption capacity varies between polymer types. Since biodegradable plastics are presented as replacements for conventional plastics in applications with risk of ending up in the marine environment, the results highlight the need to carefully examine the environmental behaviour of each biodegradable plastic type before they are extensively introduced to the market. (C) 2020 The Author(s). Published by Elsevier B.V.peerReviewe

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.Peer reviewe

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

Shifts in phytoplankton community structure modify bacterial production, abundance and community composition

In recent decades, the phytoplankton community in parts of the Baltic Sea has shifted from diatom dominance to co-occurrence of diatoms and dinoflagellates during the spring bloom. We investigated whether this shift affects bacterial production (BP), abundance and community composition (BCC). Two mesocosm experiments were carried out with water from the SW coast of Finland during the winters of 2012 and 2013. The water was collected before the onset of the spring bloom. Natural seawater was used as a control, and various inocula of diatom and dino flagellate cultures were used as treatments. After the phytoplankton bloom development, BP (thymidine: BPT; leucine: BPL) was significantly higher in the diatom treatments than in the controls and dinoflagellate treatments (BPT and BPL in 2012 and BPL in 2013). In 2013, the BCC was significantly different between the diatom and dinoflagellate treatments and there was a temporal shift in both experiments. Alphaproteobacteria predominated in all treatments at the beginning of the experiments and shifted to flavobacterial (2012) and betaproteobacterial predominance (2013) during the chlorophyll a peak. Towards the end of the experiment, Actinobacteria and Betaproteo bacteria predominated in the diatom treatment in 2012, whereas in 2013 Flavobacteriia (all treatments) predominated together with Gammaproteobacteria and Cytophagia (diatom treatments). The results demonstrated that bacterial physiology and community structure are affected by relatively small changes in the phytoplankton community. Thus, the ongoing changes in the phytoplankton community resulting from co-occurrence of diatoms and dinoflagellates may decrease pelagic remineralization of carbon and reduce organic matter fluxes through the microbial loop.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

Degradation rates and bacterial community compositions vary among commonly used bioplastic materials in a brackish marine environment

Plastic pollution threatens both terrestrial and aquatic ecosystems. As a result of the pressures of replacing oil-based materials and reducing the accumulation of litter in the environment, the use of bioplastics is increasing, despite little being known about their accurate biodegradation in natural conditions. Here, we investigated the weight attrition and degradation behavior of four different bioplastic materials compared to conventional oil-based polyethylene during a 1-year in situ incubation in the brackish Baltic Sea and in controlled 1 month biodegradation experiments in the laboratory. Bacterial communities were also investigated to verify whether putative plastic-degrading bacteria are enriched on bioplastics. Poly-l-lactic acid showed no signs of degradation, whereas poly(3-hydroxybutyrate/3-hydroxyvalerate) (PHB/HV), plasticized starch (PR), and cellulose acetate (CA) degraded completely or almost completely during 1-year in situ incubations. In accordance, bacterial taxa potentially capable of using complex carbon substrates and belonging, e.g., to class Gammaproteobacteria were significantly enriched on PHB/HV, PR, and CA. An increase in gammaproteobacterial abundance was also observed in the biodegradation experiments. The results show substantial differences in the persistence and biodegradation rates among bioplastics, thus highlighting the need for carefully selecting materials for applications with risk of becoming marine litter

Production line part of the key point incubations in part 1 (dissolved organic matter release) of the microcosm experiment, Gulf of Finland, Baltic Sea

The data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication. This data table contains measurements taken during the production line, i.e. all the measurements involving radioisotopes. It is structured based on two light and one dark measurements of primary production. Primary production measurements themselves are given in https://doi.pangaea.de/10.1594/PANGAEA.937723. From each of these subsamples (2 light and 1 dark) the following variables were measured: 14C-DOM production from 14C-NaHCO3, bacterial incorporation of 14C originating from 14C-NaHCO3, 3H-thymidine incorporation rate, and 3H-thymidine based bacterial production (calculated from thymidine incorporation rate). Raw reads from the scintillation counting are not given, only the calculated production rates calculated as explained in the methods of the associated publication. This data table is explained in figure 2 of the associated publication