Microbial Loop Dynamics in Antarctic Sea-Ice

<p>Sea-ice is a predominant feature of polar oceans and exerts a unique influence on marine ecosystems. The annual circumpolar expansion of sea-ice around Antarctica provides a stable platform for the in situ colonisation and growth of a diverse assemblage of microbes that are integral to the energy base of the Southern Ocean. An active microbial loop has been proposed to operate within the ice matrix connecting bacteria, microalgae and protozoa, but validating this metabolic pathway has historically relied on bulk correlations of chlorophyll a (a surrogate for microalgal biomass) and estimates of bacterial production or abundance. I investigate the microbial loop using a range of physiological, genetic, and ecological techniques to determine whether the photosynthate exuded by phototrophic microalgae serves as a growth substrate for heterotrophic bacteria. This link is examined at a range of spatial (in vitro and in situ experiments) and temporal (8 hours to 18 days) scales by manipulating the supply of algal-derived photosynthate and documenting the subsequent change in bacterial metabolic activity, cell abundance and community composition. Single-cell analysis of both bacterial membrane integrity and intracellular activity revealed that sea ice is among the most productive microbial habitats. In short-term in vitro experiments, increased availability of dissolved organic matter (DOM) was shown to elicit a rapid metabolic response in sea ice bacteria, however single-activity was significantly reduced in treatments where photosynthate was restricted by either removing the majority of algal cells or inhibiting photosynthesis with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). To verify this metabolic response, microcosm simulations were conducted over a period of 9 days with microbes derived from two regions of the ice (bottom layer and high-salinity surface region) with presumed differences in the concentration of DOM. Metabolic activity was relatively low in bacteria derived from the high-saline region of the ice and in cultures spiked with DCMU, photosynthate limitation restricted bacterial growth and significantly influenced community structure. In contrast, the bottom of the ice is characterised by a high concentration of DOM and bacterial metabolic activity was shown to be higher and DCMU was less influential with respect to changes in bacterial abundance or community composition. To examine in situ microbial dynamics, a series of cores were extracted from Antarctic sea-ice and reinserted into the ice matrix upside down to expose resident microbial assemblages to a significantly different light, temperature and salinity regime. Limited assimilation of algal-derived DOM by bacteria in ice cores that were flipped illustrated a malfunction in the microbial loop after a period of 18 days. Bacteria originally at the bottom of the sea ice appeared to be temperature-limited, while a lack of growth in cells originally at the top of the ice profile was attributed to a community dominated by slow-growing psychrophilic species. A stronger physiological response to disturbance was elicited by microalgae and significant growth was contrasted with severe bleaching and cell death. This reciprocal transplant is the first of its kind to examine the in situ sea ice community and illustrats that although microbial assemblages are similar with respect to trophic dynamics, they are also attuned to distinct regions within the ice. The bacterial assimilation of algal-derived DOM is of fundamental importance to the microbial loop and by confirming that photosynthate is a major stimulus for bacterial growth, these results provide a new and unique insight into microbial dynamics in Antarctic sea-ice.</p>

Microbial Loop Dynamics in Antarctic Sea-Ice

<p>Sea-ice is a predominant feature of polar oceans and exerts a unique influence on marine ecosystems. The annual circumpolar expansion of sea-ice around Antarctica provides a stable platform for the in situ colonisation and growth of a diverse assemblage of microbes that are integral to the energy base of the Southern Ocean. An active microbial loop has been proposed to operate within the ice matrix connecting bacteria, microalgae and protozoa, but validating this metabolic pathway has historically relied on bulk correlations of chlorophyll a (a surrogate for microalgal biomass) and estimates of bacterial production or abundance. I investigate the microbial loop using a range of physiological, genetic, and ecological techniques to determine whether the photosynthate exuded by phototrophic microalgae serves as a growth substrate for heterotrophic bacteria. This link is examined at a range of spatial (in vitro and in situ experiments) and temporal (8 hours to 18 days) scales by manipulating the supply of algal-derived photosynthate and documenting the subsequent change in bacterial metabolic activity, cell abundance and community composition. Single-cell analysis of both bacterial membrane integrity and intracellular activity revealed that sea ice is among the most productive microbial habitats. In short-term in vitro experiments, increased availability of dissolved organic matter (DOM) was shown to elicit a rapid metabolic response in sea ice bacteria, however single-activity was significantly reduced in treatments where photosynthate was restricted by either removing the majority of algal cells or inhibiting photosynthesis with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). To verify this metabolic response, microcosm simulations were conducted over a period of 9 days with microbes derived from two regions of the ice (bottom layer and high-salinity surface region) with presumed differences in the concentration of DOM. Metabolic activity was relatively low in bacteria derived from the high-saline region of the ice and in cultures spiked with DCMU, photosynthate limitation restricted bacterial growth and significantly influenced community structure. In contrast, the bottom of the ice is characterised by a high concentration of DOM and bacterial metabolic activity was shown to be higher and DCMU was less influential with respect to changes in bacterial abundance or community composition. To examine in situ microbial dynamics, a series of cores were extracted from Antarctic sea-ice and reinserted into the ice matrix upside down to expose resident microbial assemblages to a significantly different light, temperature and salinity regime. Limited assimilation of algal-derived DOM by bacteria in ice cores that were flipped illustrated a malfunction in the microbial loop after a period of 18 days. Bacteria originally at the bottom of the sea ice appeared to be temperature-limited, while a lack of growth in cells originally at the top of the ice profile was attributed to a community dominated by slow-growing psychrophilic species. A stronger physiological response to disturbance was elicited by microalgae and significant growth was contrasted with severe bleaching and cell death. This reciprocal transplant is the first of its kind to examine the in situ sea ice community and illustrats that although microbial assemblages are similar with respect to trophic dynamics, they are also attuned to distinct regions within the ice. The bacterial assimilation of algal-derived DOM is of fundamental importance to the microbial loop and by confirming that photosynthate is a major stimulus for bacterial growth, these results provide a new and unique insight into microbial dynamics in Antarctic sea-ice.</p>

Geological processes mediate a subsurface microbial loop in the deep biosphere

The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores1,2. Whereas dormancy and survival at theoretical energy minima are hallmarks of subsurface microbial populations3, the roles of fundamental ecological processes like dispersal and selection in these environments are poorly understood4. Here we combine geophysics, geochemistry, microbiology and genomics to investigate biogeography in the subsurface, focusing on bacterial endospores in a deep-sea setting characterized by thermogenic hydrocarbon seepage. Thermophilic endospores in permanently cold seabed sediments above petroleum seep conduits were correlated with the presence of hydrocarbons, revealing geofluid-facilitated cell migration pathways originating in deep oil reservoirs. Genomes of thermophilic bacteria highlight adaptations to life in anoxic petroleum systems and reveal that these dormant populations are closely related to oil reservoir microbiomes from around the world. After transport out of the subsurface and into the deep-sea, thermophilic endospores re-enter the geosphere by sedimentation. Viable thermophilic endospores spanning the top several metres of the seabed correspond with total endospore counts that are similar to or exceed the global average. Burial of dormant cells enables their environmental selection in sedimentary formations where new petroleum systems establish, completing a geological microbial loop that circulates living biomass in and out of the deep biosphere.

Microbial loop of a Proterozoic ocean analogue

Meromictic Lake Cadagno, an ancient ocean analogue, is known for its permanent stratification and persistent anoxygenic microbial bloom within the chemocline. Although the anaerobic microbial ecology of the lake has been extensively studied for at least 25 years, a comprehensive picture of the microbial food web linking the bacterial layer to phytoplankton and viruses, with explicit measures of primary and secondary production, is still missing. This study sought to understand better the abundances and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified zones of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested the presence of eukaryotic phytoplankton through the water column. Evidence supported high abundances of Ankyra judayi, a high-alpine adapted chlorophyte, in the oxic mixolimnion where oxygenic-primary production peaked. Through the low- and no-oxygen chemocline and monimolimnion, chlorophytes related to Closteriopsis acicularis, a known genus of meromictic lakes, and Parachlorella kessleri were observed. Chromatium, anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline suggesting primary producers depend on heterotrophs for nutrient remineralization. As previously observed, sulfur-reducing bacteria (SRBs), especially Desulfocapsa and Desulfobulbus, were present in the chemocline and anoxic monimolimnion. Virus-to-microbe ratios (VMR) peaked in the zone of phytoplankton yet were at a minimum at the peak of Chromatium. These dynamic trends suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno and other permanently stratified systems.ImportanceAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

Impact of dust addition on the microbial food web under present and future conditions of pH and temperature

In the oligotrophic waters of the Mediterranean Sea, during the stratification period, the microbial loop relies on pulsed inputs of nutrients through atmospheric deposition of aerosols from both natural (Saharan dust) and anthropogenic origins. While the influence of dust deposition on microbial processes and community composition is still not fully constrained, the extent to which future environmental conditions will affect dust inputs and the microbial response is not known. The impact of atmospheric wet dust deposition was studied both under present and future (warming and acidification) environmental conditions through experiments in 300 L climate reactors. Three dust addition experiments were performed with surface seawater collected from the Tyrrhenian Sea, Ionian Sea and Algerian basin in the Western Mediterranean Sea during the PEACETIME cruise in May–June 2017. Top-down controls on bacteria, viral processes and community, as well as microbial community structure (16S and 18S rDNA amplicon sequencing) were followed over the 3–4 days experiments. Different microbial and viral responses to dust were observed rapidly after addition and were most of the time higher when combined to future environmental conditions. The input of nutrients and trace metals changed the microbial ecosystem from bottom-up limited to a top-down controlled bacterial community, likely from grazing and induced lysogeny. The composition of mixotrophic microeukaryotes and phototrophic prokaryotes was also altered. Overall, these results suggest that the effect of dust deposition on the microbial loop is dependent on the initial microbial assemblage and metabolic state of the tested water, and that predicted warming, and acidification will intensify these responses, affecting food web processes and biogeochemical cycles.

Scaling down the microbial loop: data-driven modelling of growth interactions in a diatom-bacterium co-culture

An intricate set of interactions characterizes marine ecosystems. One of the most important is represented by the so-called microbial loop, which includes the exchange of dissolved organic matter (DOM) from phototrophic organisms to heterotrophic bacteria. Here, it can be used as the major carbon and energy source. Arguably, this interaction is one of the foundations of the entire ocean food-web. Carbon fixed by phytoplankton can be redirected to bacterial cells in two main ways; either i) bacteria feed on dead (eventually lysed) phytoplankton cells or ii) DOM is actively released by phytoplankton cells (a widespread process that may result in up to 50% of the fixed carbon leaving the cell). In this work, we have set up a co-culture of the model diatom Phaeodactylum tricornutum and the model chemoheterotrophic bacterium Pseudoalteromonas haloplanktis TAC125 and used this system to study the interactions between these two representatives of the microbial loop. We show that the bacterium can indeed thrive on diatom-derived carbon and that this growth can be sustained by both diatom dead cells and diatom-released compounds. These observations were formalized in a network of putative interactions between P. tricornutum and P. haloplanktis and implemented in a mathematical model that reproduces the observed co-culture dynamics, suggesting that our hypotheses on the interactions occurring in this two-player system can accurately explain the experimental data.