Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter

Peer reviewe

Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord

A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean’s interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump

Exploring gene expression responses of marine bacteria to environmental factors

Bacterioplankton are abundant in marine ecosystems, where they as “masters of transformation” of dissolved organic matter (DOM) are important for energy fluxes and biogeochemical cycles. However, the performance of bacteria in a changing marine environment influenced by anthropogenic activities is poorly understood. In this thesis, I did experiments with model bacteria and natural assemblages of bacteria, using microbiology methods combined with modern molecular tools, to investigate responses of marine bacteria to changes in environmental conditions like ocean acidification, organic pollution and organic matter released by phytoplankton. Experiments with a model gammaproteobacterium demonstrated that bacteria in stationary phase showed little responses to organic pollutants, whereas pollutants caused decreased bacterial growth and had a broad physiological impact on actively growing bacteria (as deduced from gene expression analysis). In an experiment with two distantly related marine model bacteria, we identified several important bacterial mechanisms, such as uptake of macromolecules and phosphonates, by which bacteria respond when exposed to DOM produced by photosynthetic dinoflagellates. Using natural bacterial communities in a Baltic Sea mesocosm experiment with the addition of river water from a forested or an agriculture influenced catchment area, we showed important interactions between river water type and the development of phytoplankton blooms that caused different bacterial gene expression activities. In the fourth set of experiments, marine bacterial communities were subjected to elevated CO2, to mimic ocean acidification, under high and low nutrient conditions in a mesocosm study. We found increased bacterial gene expression activity focused on maintaining pH homeostasis, but only under low nutrient conditions, indicating that bacteria focus on cell maintenance instead of growth when challenged by lowered pH. Finally, in a computational analysis, we compared genomes from yet uncultivated prokaryotes by two different strategies: metagenome assembled and single amplified genomes. Importantly, the analysis showed that both methods selected abundant taxa and generated nearly identical sequences in overlapping regions. To conclude, this thesis presents discoveries that will help form a better understanding of marine bacterial responses to present and future anthropogenic disturbances of marine ecosystems.Marina bakterier är abundanta och återfinns i alla marina ekosystem, där de som nedbrytare av organiskt material spelar en avgörande roll i att reglera flödet av energi och näringsämnenas kretslopp. Dock saknar vi kunskap om hur bakterieplankton reagerar på miljöförändringar i haven. Därtill är de molekylära mekanismerna för omsättningen av löst organiskt material från olika källor ofullständigt kända. I denna avhandling har jag med hjälp av bakterieisolat och naturliga bakteriesamhällen undersökt hur marina bakterier svarar på miljöförändringar genom att kombinera metoder inom klassisk mikrobiologi och moderna molekylärbiologiska verktyg. Det övergripande syftet med denna avhandling var att få en bättre förståelse för hur bakterier svarar på havsförsurning, organiska föroreningar och löst organisk kol utsöndrat av växtplankton. Under ett experiment med ett bakterieisolat inom klassen Gammaproteobacteria, uppvisade bakterierna svagare respons för organiska föroreningar då de befann sig i stationär fas än i en aktiv tillväxtfas. Detta märktes både genom minskad tillväxt och fysiologiska ändringar uppmätta genom genuttryck i bakterien. Vidare experiment med två skilda modellbakterier kunde vi identifiera viktiga processer såsom upptag av makromolekyler och fosfonater, som svar på tillsats av löst organiskt material producerat av dinoflagellater. I ett annat experiment använde vi naturliga bakteriesamhällen i vatten från Östersjön i ett storskaligt experiment, där vatten från floder i avrinningsområden dominerade antingen av skog eller jordbruk tillsattes. I detta experiment kunde vi visa hur vattnets ursprung påverkade utvecklingen av algblomningarna som i sin tur orsakade olika aktivitet i bakteriernas genuttryck. Vidare så undersöktes hur marina bakteriesamhällen påverkas av förhöjda CO2-halter under låg och hög näringstillgång. Det visade sig att bakterierna ökade sin aktivitet för att bibehålla pH-homeostasen, men bara under låg koncentration av näringsämnen. Detta innebar att bakterierna behövde ställa om sin ämnesomsättning från tillväxt till att lägga energi på att hantera syran i oligotrofa miljöer. Slutligen genomfördes dataanalyser där två metoder för att studera arvsmassan i bakterier tagna direkt från haven jämfördes. Vår studie visade att de två metoderna i viss mån kompletterade varandra men framför allt kunde vi bekräfta att ingen av de två uppvisade några systematiska fel. Sammanfattningsvis presenterar denna avhandling upptäcker som ger oss en bättre förståelse för hur marina bakterier i marina ekosystem svarar på nutida och framtida miljöförändringar orsakade av människor

Composition and Seasonality of Membrane Transporters in Marine Picoplankton

In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3μm–0.2μm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models

Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak

The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3–V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml–1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord

Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak

The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 x 10(4) cells ml(-1). This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord

Dynamics of Baltic Sea phages driven by environmental changes

Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms