High nutrient transport and cycling potential revealed in the microbial metagenome of australian sea lion (neophoca cinerea) faeces

Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production. © 2012 Lavery et al

Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats

Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance

Spatially varying complexity of bacterial and viruslike particle communities within an aquifer system

Hydrological and geological heterogeneity in the subsurface can isolate ground - water bodies in an aquifer system and create hydrologically distinct aquifers overlying each other with varying amounts of water exchange and unknown amounts of biological exchange. The hetero geneous nature of these subsurface waters likely drives changes in groundwater microbiological parameters. In the present study, flow cytometry was used to examine the abundance and cytometrically defined subpopulation structure of bacteria and virus-like particles (VLPs) in 3 distinct, vertically stratified aquifer layers consisting of an unconfined aquifer, a confining layer and a confined aquifer. Despite total microbial abundances remaining constant, the composition of bacterial and VLP communities varied among the aquifer layers. Cytometrically defined subpopulations were defined by nucleic acid content and size and ranged from 1 bacterial and VLP subpopulation in the unconfined aquifer to 4 bacterial and 3 VLP subpopulations in the confined aquifer. This variability in the subpopulation assemblages is likely driven by a combination of hydrological heterogeneity and biological interactions. The results presented here indicate complexity in microbial communities in discrete aquifer layers that may be overlooked when reporting general abundances. Groundwater bacteria and VLPs appear to be a sensitive indicator of the biological dynamics of aquifer systems and may be used to identify heterogeneous water bodies and help distinguish individual aquifer layers in an aquifer system. Copyright © Inter-Research 2013

Can whales mix the ocean?

International audienceOcean mixing influences global climate and enhances primary productivity by transporting nutrient rich water into the euphotic zone. The contribution of the swimming biosphere to diapycnal mixing in the ocean has been hypothesised to occur on scales similar to that of tides or winds, however, the extent to which this contributes to nutrient transport and stimulates primary productivity has not been explored. Here, we introduce a novel method to estimate the diapycnal diffusivity that occurs as a result of a sperm whale swimming through a pycnocline. Nutrient profiles from the Hawaiian Ocean are used to further estimate the amount of nitrogen transported into the euphotic zone and the primary productivity stimulated as a result. We estimate that the 80 sperm whales that travel through an area of 104 km2 surrounding Hawaii increase diapycnal diffusivity by 10-6 m2 s−1 which results in the flux of 105 kg of nitrogen into the euphotic zone each year. This nitrogen input subsequently stimulates 6 × 105 kg of carbon per year. The nutrient input of swimming sperm whales is modest compared to dominant modes of nutrient transport such as nitrogen fixation but occurs more consistently and thus may provide the nutrients necessary to enable phytoplankton growth and survival in the absence of other seasonal and daily nutrient inputs

Bacterial and virus-like particle abundances in purged and unpurged groundwater depth profiles

Bacteria and viruses are ubiquitous in subterranean aquatic habitats. Bacterial abundance is known to vary with depth in aquifers; however, whether viral abundance varies with depth is less well known. Here we use flow cytometry (FCM) to enumerate bacteria and virus-like particles (VLP) from groundwater depth profiles. Groundwater samples were obtained from a set of nested piezometers from depths of 15, 30, 45, 60, 80, and 90m and bacteria and VLP abundances were determined in purged aquifer water and unpurged water at each slot depth. Mean bacterial abundance (cells/mL) was not significantly different in unpurged water (3.2×105) compared to purged water (1.4×105); however, mean VLP abundance (particles/mL) was significantly greater in unpurged water (4.4×105) compared to purged water (2.3×105). Purged water was used to investigate the aquifer depth profile and bacterial and VLP abundances were observed to vary significantly between depths. The virus-bacteria ratio was determined and was observed to steadily increase with depth. Overall, our data indicate the dynamic nature of bacterial and viral abundances in subsurface environments which should be considered when designing groundwater microbial sampling methodologies. Ground Water Monitoring & Remediation. © 2012, National Ground Water Association

Whales sustain fisheries: Blue whales stimulate primary production in the Southern Ocean

It has previously been asserted that baleen whales compete with fisheries by consuming potentially harvestable marine resources. The regularly applied "surplus-yield model" suggests that whale prey becomes available to fisheries if whales are removed, and has been presented as a justification for whaling. However, recent findings indicate that whales enhance ecosystem productivity by defecating iron that stimulates primary productivity in iron-limited waters. While juvenile whales and whales that are pregnant or lactating retain iron for growth and milk production, nonbreeding adult whales defecate most of the iron they consume. Here, we modify the surplus-yield model to incorporate iron defecation. After modeling a simplistic trajectory of blue whale recovery to historical abundances, the traditional surplus-yield model predicts that 1011 kg of carbon yr-1 would become unavailable to fisheries. However, this ignores the nutrient recycling role of whales. Our model suggests the population of blue whales would defecate 3 × 106 kg of iron yr-1, which would stimulate primary production equivalent to that required to support prey consumption by the blue whale population. Thus, modifying the surplus-yield model to include iron defecation indicates that blue whales do not render marine resources unavailable to fisheries. By defecating iron-rich feces, blue whales promote Southern Ocean productivity, rather than reducing fishery yields. © 2014 Society for Marine Mammalogy

Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems

A metagenomic analysis of two aquifer systems located under a dairy farming region was performed to examine to what extent the composition and function of microbial communities varies between confined and surface-influenced unconfined groundwater ecosystems. A fundamental shift in taxa was seen with an overrepresentation of Rhodospirillales, Rhodocyclales, Chlorobia and Circovirus in the unconfined aquifer, while Deltaproteobacteria and Clostridiales were overrepresented in the confined aquifer. A relative overrepresentation of metabolic processes including antibiotic resistance (β-lactamase genes), lactose and glucose utilization and DNA replication were observed in the unconfined aquifer, while flagella production, phosphate metabolism and starch uptake pathways were all overrepresented in the confined aquifer. These differences were likely driven by differences in the nutrient status and extent of exposure to contaminants of the two groundwater systems. However, when compared with freshwater, ocean, sediment and animal gut metagenomes, the unconfined and confined aquifers were taxonomically and metabolically more similar to each other than to any other environment. This suggests that intrinsic features of groundwater ecosystems, including low oxygen levels and a lack of sunlight, have provided specific niches for evolution to create unique microbial communities. Obtaining a broader understanding of the structure and function of microbial communities inhabiting different groundwater systems is particularly important given the increased need for managing groundwater reserves of potable water.Renee J. Smith, Thomas C. Jeffries, Ben Roudnew, Alison J. Fitch, Justin R. Seymour, Marina W. Delpin, Kelly Newton, Melissa H. Brown, and James G. Mitchel

Iron defecation by sperm whales stimulates carbon export in the Southern Ocean.

The iron-limited Southern Ocean plays an important role in regulating atmospheric CO2 levels. Marine mammal respiration has been proposed to decrease the efficiency of the Southern Ocean biological pump by returning photosynthetically fixed carbon to the atmosphere. Here, we show that by consuming prey at depth and defecating iron-rich liquid faeces into the photic zone, sperm whales (Physeter macrocephalus) instead stimulate new primary production and carbon export to the deep ocean. We estimate that Southern Ocean sperm whales defecate 50 tonnes of iron into the photic zone each year. Molar ratios of Cexport : Feadded determined during natural ocean fertilization events are used to estimate the amount of carbon exported to the deep ocean in response to the iron defecated by sperm whales. We find that Southern Ocean sperm whales stimulate the export of 4 × 105 tonnes of carbon per year to the deep ocean and respire only 2 × 10 5 tonnes of carbon per year. By enhancing new primary production, the populations of 12 000 sperm whales in the Southern Ocean act as a carbon sink, removing 2 × 105 tonnes more carbon from the atmosphere than they add during respiration. The ability of the Southern Ocean to act as a carbon sink may have been diminished by large-scale removal of sperm whales during industrial whaling. © 2010 The Royal Society