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This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.

We used stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopes to assess the importance of benthic algae for the zooplankton individual growth in winter in a shallow, clear subarctic lake. The δ¹³C values of calanoid (Eudiaptomus graciloides) and cyclopoid (Cyclops scutifer) zooplankton in autumn suggest a food resource of pelagic origin during the ice-free period. The zooplankton δ¹³C values were high in spring compared to autumn. E. graciloides did not grow over winter and the change in δ¹³C was attributed to a decrease in lipid content during the winter. In contrast, the increase in δ¹³C values of C. scutifer over the winter was explained by their growth on organic carbon generated by benthic algae. The δ¹⁵N of the C. scutifer food resource during winter was low compared to δ¹⁵N of the benthic community, suggesting that organic matter generated by benthic algae was mainly channelled to zooplankton via ¹⁵N-depleted heterotrophic bacteria. The results demonstrate that benthic algae can sustain zooplankton metabolic demands and growth during long winters, which, in turn, may promote zooplankton growth on pelagic resources during the summer. Such multi-chain omnivory challenges the view of zooplankton as mainly dependent on internal primary production and stresses the importance of benthic resources for the productivity of plankton food webs in shallow lakes.

We used stable carbon (5 13 C) and nitrogen (5 15 N) isotopes to assess the importance of benthic algae for the zooplankton individual growth in winter in a shallow, clear subarctic lake. The 8 13 C values of calanoid (Eudiaptomus graciloides) and cyclopoid (Cyclops scutifer) zooplankton in autumn suggest a food resource of pelagic origin during the ice-free period. The zooplankton 5 13 C values were high in spring compared to autumn. E. graciloides did not grow over winter and the change in 5 13 C was attributed to a decrease in lipid content during the winter. In contrast, the increase in 5 13 C values of C. scutifer over the winter was explained by their growth on organic carbon generated by benthic algae. The 8 15 N of the C. scutifer food resource during winter was low compared to 8 15 N of the benthic community, suggesting that organic matter generated by benthic algae was mainly channelled to zooplankton via 15 N-depleted heterotrophic bacteria. The results demonstrate that benthic algae can sustain zooplankton metabolic demands and growth during long winters, which, in turn, may promote zooplankton growth on pelagic resources during the summer. Such multi-chain omnivory challenges the view of zooplankton as mainly dependent on internal primary production and stresses the importance of benthic resources for the productivity of plankton food webs in shallow lakes.

Microorganisms play a critical role in nitrogen cycling by mineralising dissolved organic nitrogen (DON) compounds into bioavailable inorganic forms (DIN). Although DIN is crucial for seagrass growth, the hypothesis that seagrass leaf associated-microorganisms could convert DON to forms available for plant uptake has never been tested. We conducted a laboratory-based experiment in which seagrass ( Posidonia sinuosa ) leaves were incubated with 15 N-amino acids (aa), with and without associated microorganisms. Samples were collected after 0.5, 2, 6 and 12 h. Both bulk stable isotope and nanoscale secondary ion mass spectrometry (NanoSIMS) analysis showed high accumulation of 15 N within seagrass leaf tissues with an associated microbiota, but not in plants devoid of microorganisms. These results significantly change our understanding of the mechanisms of seagrass nitrogen use and provide evidence that seagrass microbiota increase nitrogen availability for uptake by seagrass leaves by mineralising aa, thus enhancing growth and productivity of these important coastal ecosystems.

The Western Rocklobster (Panulirus cygnus) is the most valuable single species fishery in Australia and the largest single country spiny lobster fishery in the world. In recent years a well-known relationship between oceanographic conditions and lobster recruitment has become uncoupled, with significantly lower recruitment than expected, generating interest in the factors influencing survival and development of the planktonic larval stages. The nutritional requirements and wild prey of the planktotrophic larval stage (phyllosoma) of P. cygnus were previously unknown, hampering both management and aquaculture efforts for this species. Ship-board feeding trials of wild-caught mid-late stage P. cygnus phyllosoma in the eastern Indian Ocean, off the coast of Western Australia, were conducted in July 2010 and August-September 2011. In a series of experiments, phyllosoma were fed single and mixed species diets of relatively abundant potential prey items (chaetognaths, salps, and krill). Chaetognaths were consumed in 2–8 times higher numbers than the other prey, and the rate of consumption of chaetognaths increased with increasing concentration of prey. The highly variable lipid content of the phyllosoma, and the fatty acid profiles of the phyllosoma and chaetognaths, indicated they were from an oligotrophic oceanic food chain where food resources for macrozooplankton were likely to be constrained. Phyllosoma fed chaetognaths over 6 days showed significant changes in some fatty acids and tended to accumulate lipid, indicating an improvement in overall nutritional condition. The discovery of a preferred prey for P. cygnus will provide a basis for future oceanographic, management and aquaculture research for this economically and ecologically valuable species.

Anticyclonic (warm-core) mesoscale eddies (WCEs) in the Eastern Indian Ocean carry higher surface chlorophyll signatures than cyclonic (cold-core) eddies (CCEs). Paradoxically, WCEs host rock lobster larvae (phyllosomas) with lower lipid stores and protein reserves than phyllosomas in CCEs, suggesting a poorer nutritional status. We assess primary productivity and zooplankton isotopic data from eight eddies across four research voyages (2003–2011) to determine how this contradiction might occur. We find that WCEs and CCEs are equally productive per unit chlorophyll a, but depth-integrated primary production (PP) is greater in eddies with shallower mixed layers (MLs), especially in CCEs. MLs tend to be shallower in CCEs than in WCEs because the pycnocline is closer to the surface. This, in combination with stronger stratification in CCE euphotic zones than those of WCEs, supports greater flagellate and dinoflagellate populations in CCEs. These phytoplankton provide high-quality nutrition for zooplankton, which feed on average ~ 0.6 trophic level lower in CCEs with the shallowest MLs, accumulating high lipid stores. Conversely, WCEs have, on average, ~ 70 m deeper MLs than CCEs, and host a phytoplankton community with more diatoms. Diatoms provide lower quality food for zooplankton, and zooplankton lipid stores in WCEs decline with trophic level, and possibly, with time after initial (or seasonal) nutrient injection. As a result, phyllosomas in CCEs have higher energy and lipid content than those in warm-core eddies. The resolution of the paradox, therefore, is that the higher surface chlorophyll signatures of WCEs are not representative of the nutritional value of the prey field of the phyllosoma. We also conclude that interannual variations of mixed layer depth occur at a regional scale, controlling PP.

Virus-bacterium interactions were investigated in the pelagic and benthic habitats in a set of lakes along an altitudinal gradient in the subarctic northern Sweden. Viral and bacterial abundances showed a significant variation between the lakes, with the highest benthic microbial abundances recorded in a high-altitude lake [993 m above sea level (a.s.l.)], whereas the highest pelagic microbial abundances were found in a low-altitude lake (270 m a.s.l.). In the pelagic habitat, there was also a distinct difference in microbial abundances between the summer-autumn and the winter sampling occasion. A positive relationship was noted between viruses and bacteria in both the pelagic and the benthic habitats. Visibly virus-infected bacterial cells were uncommon in the pelagic habitat and undetectable in the benthos. Both lytic and lysogenic pelagic viral production rates were undetectable or low; thus, a possible explanation for the relative high viral abundances found in the water column could be an allochthonous input of viruses or release of sediment-derived viruses. Overall, our results provide novel information about the relevance of viruses in the subarctic region and indicate that viruses play only a minor role in the nutrient and carbon cycling in the microbial communities of subarctic lakes.

The microbial communities and photosynthetic capacity of cryoconite holes on the Midre Lovénbreen Glacier at 79°N in Spitzbergen (Svalbard Archipelago) were investigated in July/August 2000 and July 2001. The constituents of the microbial assemblages were more abundant in material on the cryoconite bottoms than in the overlying water. Bacterial concentrations ranged from 1.00 to 4.50×10^sup 4^ ml^sup -1^ in the water and from 4.67 to 7.07×10^sup 4^ ml^sup -1^ in the bottom material; virus-like particles (VLP) ranged from 3.97 to 12.70×10^sup 4^ml^sup -1^ in the water and from 27.5 to 37.59×10^sup 4^ ml^sup -1^ on the bottom. VLP: bacteria ratios ranged between 0.24 and 8.11, with highest ratios in the bottom assemblages. Heterotrophic nanoflagellate (HNAN) abundances were significantly lower than those of the autotrophic nanoflagellates (PNAN). Moreover, HNAN biomass was lower than bacterial biomass, indicating that the HNAN were exploiting other energy sources as well as bacteria, for example, VLP and dissolved organic carbon. The bottom material was dominated by cyanobacteria (mostly Phormidium sp.), while both the water and the bottom layer contained a small number of chlorophyte species (Chlorella sp., Cylindromonas sp. and Chlamydomonas nivalis). Ciliates were very sparse, only occurring on the bottom. On occasions, the glacier surface carried meltwater with well-developed biofilms, in which ciliates (Monodinium, Strombidium and Halteria) occurred. All of these species are found in nearby lakes. One to three rotifers were noted in the biofilm samples and in samples from three of the cryoconite holes. The assemblages of the cryoconite holes were comparable to the truncated food webs seen in Antarctic lakes, but were even more simplified and sparse in terms of biomass. Photosynthesis in the meltwater on the glacier surface ranged between 0.60 and 8.33 µg C l^sup -1^ h^sup -1^. Within the cryoconites, photosynthetic rates were usually highest on the bottom (0.63-156.99 µg C l^sup -1^ h^sup -1^), while in the overlying water, rates ranged between 0.34 and 10.56 µg C l^sup -1^ h^sup -1^. Given the density of cryoconite holes (circa 6% of the glacier surface, or 12 holes m^sup -2^), there was significant carbon fixation and nutrient cycling occurring on the glacier, associated with cryoconite communities.[PUBLICATION ABSTRACT]

The effect of viruses on the microbial loop, with particular emphasis on bacteria, was investigated over an annual cycle in 2003-2004 in Lake Druzhby and Crooked Lake, two large ultraoligotrophic freshwater lakes in the Vestfold Hills, Eastern Antarctica. Viral abundance ranged from 0.16 to 1.56 x 10⁹ particles L⁻¹;¹ and bacterial abundances ranged from 0.10 to 0.24 x 10⁹ cells L⁻¹;¹, with the lowest bacterial abundances noted in the winter months. Virus-to-bacteria ratios (VBR) were consistently low in both lakes throughout the season, ranging from 1.2 to 8.4. lysogenic bacteria, determined by induction with mitomycin C, were detected on three sampling occasions out of 10 in both lakes. In Lake Druzhby and Crooked Lake, lysogenic bacteria made up between 18% and 73% of the total bacteria population during the lysogenic events. Bacterial production ranged from 8.2 to 304.9 x 10⁶ cells L⁻¹;¹ day⁻¹;¹ and lytic viral production ranged from 47.5 to 718.4 x 10⁶ viruslike particles L⁻¹;¹ day⁻¹;¹. When only considering primary production, heterotrophic nanoflagellate (HNF) grazing and viral lysis as the major contributors to the DOC pool (i.e., autochthonous sources), we estimated a high contribution from viruses during the winter months when >60% of the carbon supplied to the DOC pool originated from viral lysis. In contrast, during the summer <20% originated from viral lysis. Our study shows that viral process in ultraoligotrophic Antarctic lakes may be of quantitative significance with respect to carbon flow especially during the dark winter period.

Microbes are ubiquitous but our knowledge of their effects on consumers is limited in benthic marine systems. Shorelines often form hotspots of microbial and detritivore activity due to the large amounts of detrital macrophytes that are exported from other coastal ecosystems, such as kelp forests, and accumulate in these systems. Shoreline ecosystems therefore provide a useful model system to examine microbial-detritivore interactions. We experimentally test whether bacteria in the biofilm of kelp provide a bottom-up influence on growth and reproductive output of detritivores in shorelines where detrital kelp accumulates, by manipulating the bacterial abundances on kelp ( Ecklonia radiata ). The growth rates for both male and female amphipods ( Allorchestes compressa ) were greater in treatments containing bacteria than those in which bacteria were reduced through antibiotic treatment, and this effect was greater for males offered aged kelp. The proportions of ovigerous females were greater when reared on kelp with intact bacteria, indicating a more rapid reproductive development in the presence of more bacteria. Bacterial abundance had little to no influence on nutrient content and palatability of kelp, based on tissue toughness, nitrogen and carbon content and C:N ratio. Thus, the most likely pathway for a microbial effect on detritivores was through feeding on kelp-associated bacteria. Regardless of the pathway, kelp-associated microbes have a strong influence on the fitness of a highly abundant detritivore that feeds preferentially on E. radiata in shoreline systems, and therefore form a hidden trophic step in this “brown” food web and a hotspot of secondary production.