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A universal scaling relationship exists between organism abundance and body size1,2. Within ocean habitats this relationship deviates from that generally observed in terrestrial systems2–4, where marine macro-fauna display steeper size-abundance scaling than expected. This is indicative of a fundamental shift in food-web organization, yet a conclusive mechanism for this pattern has remained elusive. We demonstrate that while fishing has partially contributed to the reduced abundance of larger organisms, a larger effect comes from ocean turbulence: the energetic cost of movement within a turbulent environment induces additional biomass losses among the nekton. These results identify turbulence as a novel mechanism governing the marine size-abundance distribution, highlighting the complex interplay of biophysical forces that must be considered alongside anthropogenic impacts in processes governing marine ecosystems.

The ability of influenza A virus to evolve, coupled with increasing antimicrobial resistance, could trigger an influenza pandemic with great morbidity and mortality. Much of the 1918 influenza pandemic mortality was likely due to bacterial coinfection, including Staphylococcus aureus pneumonia. S. aureus resists many antibiotics. The lack of new antibiotics suggests alternative antimicrobials, such as bacteriophages, are needed. Potential delivery routes for bacteriophage therapy (BT) include inhalation and intravenous injection. BT has recently been used successfully in compassionate access pulmonary infection cases. Phage lysins, enzymes that hydrolyze bacterial cell walls and which are bactericidal, are efficacious in animal pneumonia models. Clinical trials will be needed to determine whether BT can ameliorate disease in influenza and S. aureus coinfection.

Flow cytometry is an established method for the detection and enumeration of viruses. However, the technique is unable to target specific viral species. Here, we present OligoFlow, a novel method for the rapid detection and enumeration of viruses by incorporating flow cytometry with species specific oligonucleotide hybridization. Using Ostried herpesvirus and dengue virus as model organisms, we demonstrate high-level detection and specificity. Our results represent a significant advancement in viral flow cytometry, opening the possibilities for the rapid identification of viruses in time critical settings.

Flow cytometry is a high-throughput tool for determining microbial abundance in a range of medical, environmental, and food-related samples. For wine, determining the abundance of Saccharomyces cerevisiae is well-defined and reliable. However, for the most common wine bacterium, Oenococcus oeni, using flow cytometry to determine cell concentration poses some challenges. O. oeni most often occurs in doublets or chains of varying lengths that can be greater than seven cells. This wine bacterium is also small, at 0.2-0.6 μm and may exhibit a range of morphologies including binary fission and aggregated complexes. This work demonstrates a straightforward approach to determining the suitability of flow cytometry for the chain-forming bacteria, O. oeni, and considerations when using flow cytometry for the enumeration of small microorganisms (

Uncovering the role of environmental factors and finding critical factors which harbor significant fractions in governing microbial communities remain key questions in coastal marine systems. To detect the interactions between environmental factors and distributions of virio- and bacterioplankton in trophic coastal areas, we used flow cytometry to investigate the abundance of virio- and bacterioplankton covering 31 stations in the Bohai Sea of China. Our results suggested that the average abundance of total virus (TV) in winter (∼2.29×108 particles/mL) was slightly lower than in summer (∼3.83×108 particles/mL). The mean total bacterial abundance (TB) was much lower in winter (∼2.54×107 particles/mL) than in summer (∼5.43×107 particles/mL). Correlation analysis via redundancy analysis (RDA) and network analysis among virioplankton, bacterioplankton and environmental factors revealed that the abundances of viral and bacterial subpopulations depend on environmental factors. In winter, only temperature significantly influenced the abundances of virio- and bacterioplankton. In summer, in addition to temperature, both salinity and nutrient (SiO2) had a remarkable impact on the distribution of virio- and bacterioplankton. Our results showed a clear seasonal and trophic pattern throughout the whole water system, which revealed that temperature and eutrophication may play crucial roles in microbial distribution pattern.

Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.

There is potential for phages to prevent and control bacterial biofilms, but few studies have examined the effect of phages on the multispecies biofilms that characterize most bacterial infections. This paper reviews the mechanism of action of phages, the evidence supporting the view that phage therapy will be effective against bacterial targets and the opposite viewpoint, phage application approaches, and the comparative advantage of phage therapy in multispecies biofilms. The few reports measuring the actions of lytic phages against multispecies biofilms are also reviewed. The authors are cautiously optimistic about the application of phages against their targets when in multispecies biofilms because some lysis mechanisms do not require species specificity.

The two most commonly used wine microorganisms,Saccharomyces cerevisiaeyeast andOenococcus oenibacteria, are responsible for completion of alcoholic and malolactic fermentation (MLF), respectively. For successful co-inoculation,S. cerevisiaeandO. oenimust be able to complete fermentation, however, this relies on compatibility between yeast and bacterial strains. For the first time, Quantitative Trait Loci (QTL) analysis was used to elucidate whetherS. cerevisiaegenetic makeup can play a role in the ability ofO. oenito complete MLF. Assessment of 67 progeny of anS. cerevisiaeSBxGN cross, co-inoculated with a singleO. oenistrain, SB3, revealed a major QTL linked to MLF completion byO. oeni. This QTL encompassed a well-known translocation, XV-t-XVI, that results in increasedSSU1expression and is functionally linked with numerous phenotypes including lag phase duration and sulfite export and production. A reciprocal hemizygosity assay was performed to elucidate the effect of the geneSSU1in the SBxGN background. Our results instead revealed a strong effect ofSSU1haploinsufficiency onO. oeni’s ability to complete malolactic fermentation during co-inoculation, and paves the way for the implementation of QTL mapping projects for deciphering the genetic bases of microbial interactions.Key pointsFor the first time QTL analysis has been used to study yeast-bacteria interactions.A QTL encompassing a translocation, XV-t-XVI, was linked to MLF outcomes.S. cerevisiae SSU1haploinsufficiency positively impacted MLF byO. oeni.

Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-Macarthur ODEs to eliminate prey-mass dependency. We define the functional response term to match experiments, and examine situations where metabolic theory derivations and observation diverge. We produce dynamics consistent with observation. Our parameterisation of the Rosenzweig-Macarthur system is an accurate minimal model across 15+ orders of mass magnitude.

The two most commonly used wine microorganisms, Saccharomyces cerevisiae yeast and Oenococcus oeni bacteria, are responsible for completion of alcoholic and malolactic fermentation (MLF), respectively. For successful co-inoculation, S. cerevisiae and O. oeni must be able to complete fermentation; however, this relies on compatibility between yeast and bacterial strains. For the first time, quantitative trait loci (QTL) analysis was used to elucidate whether S. cerevisiae genetic makeup can play a role in the ability of O. oeni to complete MLF. Assessment of 67 progeny from a hybrid S. cerevisiae strain (SBxGN), co-inoculated with a single O. oeni strain, SB3, revealed a major QTL linked to MLF completion by O. oeni. This QTL encompassed a well-known translocation, XV-t-XVI, that results in increased SSU1 expression and is functionally linked with numerous phenotypes including lag phase duration and sulphite export and production. A reciprocal hemizygosity assay was performed to elucidate the effect of the gene SSU1 in the SBxGN background. Our results revealed a strong effect of SSU1 haploinsufficiency on O. oeni's ability to complete malolactic fermentation during co-inoculation and pave the way for the implementation of QTL mapping projects for deciphering the genetic bases of microbial interactions. KEY POINTS: • For the first time, QTL analysis has been used to study yeast-bacteria interactions. • A QTL encompassing a translocation, XV-t-XVI, was linked to MLF outcomes. • S. cerevisiae SSU1 haploinsufficiency positively impacted MLF by O. oeni.

The ability of influenza A virus to evolve, coupled with increasing antimicrobial resistance, could trigger an influenza pandemic with great morbidity and mortality. Much of the 1918 influenza pandemic mortality was likely due to bacterial coinfection, including

High rate algal ponds (HRAPs) are shallow, mixed systems for wastewater treatment, which use sunlight exposure for disinfection. Little is known regarding the relationships between the bacteria and viruses within HRAP systems. Uniquely, flow cytometry permits the rapid identification of bacterial and viral populations in wastewater samples, separating populations based on genome and particle size. Treated wastewater samples were collected from an HRAP at Kingston on Murray, South Australia. Flow cytometry analysis detected bacterial populations and discriminated virus-like particles (VLP) and large VLP (LVLP). Rapid, short term, fluctuations in the abundance of all three populations were observed. Changes in the abundance of these populations was compared; wastewater composition was used as metadata for the comparisons. Linear regression determined relationships in abundances between bacteria and LVLP (R2 0.2985); LVLP and VLP (R2 0.5829) and bacteria and VLP (R2 0.5778) all with p-values of

BackgroundDiabetic foot ulcer (DFU) is a serious complication of diabetes mellitus. Antibiotic-resistantStaphylococcus aureusis frequently isolated from DFU infections. Bacteriophages (phages) represent an alternative or adjunct treatment to antibiotic therapy. Here we describe the efficacy of AB-SA01, a cocktail of threeS. aureus Myoviridaephages, made to current good manufacturing practice (cGMP) standards, and which has undergone two phase I clinical trials, in treatment of multidrug-resistant (MDR)S. aureusinfections.ResultsWounds of saline-treated mice showed no healing, but expanded and became inflamed, ulcerated, and suppurating. In contrast, AB-SA01 treatment decreased the bacterial load with efficacy similar or superior to vancomycin treatment. At the end of the treatment period, there was a significant decrease (p ConclusionTopical application of phage cocktail AB-SA01 is effective, as shown by bacterial load reduction and wound closure, in the treatment of diabetic wound infections caused by MDRS. aureus. Our results suggest that topical phage cocktail treatment may be effective in treating antibiotic-resistantS. aureusDFU infections.

Environmental conditions shape entire communities by driving microbial interactions. These interactions then find their reflection in the evolutionary outcome of microbial competition. In static, homogeneous environments a robust, or evolutionary stable, outcome in microbial communities is reachable, if it exists. However, introducing heterogeneity and time-dependence in microbial ecology leads to stochastic evolutionary outcomes determined by specific environmental changes. We utilise evolutionary game theory to provide insight into phenotypic competition in dynamic environments. We capture these effects in a perturbed evolutionary game describing microbial interactions at a phenotypic level. We show that under regular periodic environmental fluctuations a stable state that preserves dominant phenotypes is reached. However, rapid environmental shifts, especially in a cyclic interactions, can lead to critical shifts in the evolutionary balance among phenotypes. Our analysis suggests that an understanding of the robustness of the systems current state is necessary to understand when system will shift to the new equilibrium. This can be done by understanding the systems overall margin of safety, that is, what level of perturbations it can take before its equilibrium changes. In particular, the extent to which an environmental shift affects the system’s behaviour.

Objective: Microhabitats in the oral cavity differ in microbial taxonomy. However, abundance variations of bacterial and viral communities within these microhabitats are not fully understood.Aims and Hypothesis: To assess the spatial distribution and dynamics of the microbial abundances within 6 microhabitats of the oral cavity before and after sleep. We hypothesise that the abundance distributions of these microbial communities will differ among oral sites.Methods: Using flow cytometry, bacterial and virus-like particle (VLP) abundances were enumerated for 6 oral microhabitats before and after sleep in 10 healthy paediatric sleepers.Results: Bacterial counts ranged from 7.2 ± 2.8 × 105 at the palate before sleep to1.3 ± 0.2 × 108 at the back of the tongue after sleep, a difference of 187 times. VLPs ranged from 1.9 ± 1.0 × 106 at the palate before sleep to 9.2 ± 5.0 × 107 at the back of the tongue after sleep, a difference of 48 times.Conclusion: The oral cavity is a dynamic numerically heterogeneous environment where microbial communities can increase by a count of 100 million during sleep. Quantification of the paediatric oral microbiome complements taxonomic diversity information to show how biomass varies and shifts in space and time. Refereed/Peer-reviewed

The composition and diversity of bacteria forming the microbiome of parasitic organisms have implications for differential host pathogenicity and host-parasite co-evolutionary interactions. The microbiome of pathogens can therefore have consequences that are relevant for managing disease prevalence and impact in affected hosts. Here we investigate the microbiome of an invasive parasitic fly Philornis downsi, recently introduced to the Galapagos Islands, where it poses extinction threat to Darwin's finches and other land birds. Larvae infest nests of Darwin's finches and consume blood and tissue of developing nestlings, and have severe mortality impacts. Using 16s rRNA sequencing data we characterize the bacterial microbiota associated with P. downsi adults and larvae sourced from four finch host species, inhabiting two islands and representing two ecologically distinct groups. We show that larval and adult microbiomes are dominated by the phyla Proteobacteria and Firmicutes, which significantly differ between life stages in their distributions. Additionally, bacterial community structure significantly differed between larvae retrieved from strictly insectivorous warbler finches (Certhidea olivacea) and those parasitizing hosts with broader dietary preferences (ground and tree finches, Geospiza and Camarhynchus spp. respectively). Finally, we found no spatial effects on the larval microbiome, as larvae feeding on the same host (ground finches) harbored similar microbiomes across islands. Our results suggest that the microbiome of P. downsi changes during its development, according to dietary composition or nutritional needs, and is significantly affected by host-related factors during the larval stage. Unraveling the ecological significance of bacteria for this parasite will contribute to the development of novel, effective control strategies. This article is protected by copyright. All rights reserved.

Bacteria are ubiquitous on the Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses and chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain, but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting that successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show that microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology, and disease development by setting the initial conditions that determine the winners as a community develops.

Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3–10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

The rectilinear "drift" of particles in a hydrodynamic drift ratchet arises from a combination of diffusive motion and particle-wall hydrodynamic interactions, and is therefore dependent on particle diffusivity, particle size, the amplitude and frequency of fluid oscillation and pore geometry. Using numerical simulations, we demonstrate that the drift velocity relative to the pore size is constant across different sized drift ratchet pores, if all the relevant non-dimensional groups (Peclet number, Strouhal number and ratio of particle to pore size) remain constant. These results clearly indicate for the first time the scaling parameters under which the drift ratchet achieves dynamic similarity, and so facilitates design, fabrication and testing of drift ratchets for experiments and eventually as commercial micro/nano fluidic separation devices., 17 pages, 10 figures

Microscale microbial distributions are patchy, with abundance hotspots and coldspots that provide important microenvironments for microbial interactions. However, studies are often restricted to abundance estimates alone. At the riverbed of the Murray River, we used taxonomy to complement quantitative analysis to show that abundance hotspots, coldspots and background levels are taxonomically distinct at all taxonomic levels. Abundance hotspots varied 115- and 5.9-fold above background over 0.9 cm for viruses and bacteria, respectively. For bacteria, hotspots represent increases in particular taxa rather than in all bacteria. Genera with increased abundances—Pseudomonas, Parasporobacterium, Lachnospiraceae incertae sedis and Bacteroides—were indicative of human and animal inputs, and represented up to 14.7% of the community. Distinct dominant genera led to high taxonomic dissimilarity among hotspots. Genera exclusivity was still higher in the background and coldspots, with 54 and 48 exclusive genera compared to 7 and 4 genera in hotspots, suggesting hotspots from persistent genera, rather than introduced genera. Hotspots were more similar to coldspots than background, suggesting coldspots may represent dying hotspots. Sample category predicted taxonomic similarity better than proximity, further indicating these heterogeneities are distinct from the background at the sub-centimetre scale. Hotspots and coldspots represent distinct spatial taxonomic distributions, rather than changes of the overall community. This suggests 0.3 ml volumes are cohesive long enough for particular operational taxonomic units (OTUs) to increase and create taxonomically distinct microscale communities within the Kolmogorov and Batchelor scales.

The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These "phycospheres" may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean.

Identifying members of the aquatic microbial community and their biotic and abiotic interactions are the first step in developing inocula for bio-floc starters used as aquaculture fish-feed. This research aims to identify whether a freshwater river with urban input can be used as a source of potential bio-floc forming bacteria. To identify the bacteria, 16S rDNA sequencing was performed, to determine the taxonomy and flow cytometry was employed to enumerate bacterial abundance. To resolve the complex interactions among microbes, microbial interaction networks were produced at the family level. Actinobacteria was found to be the most abundant bacterial phylum followed by Proteobacteria, Acidobacteria, and Chloroflexi that suggested the river was in health condition. Microbial interaction networks revealed nutrients, particularly nitrate, nitrite, ammonia, and silica, are crucial in maintaining network interactions, suggesting that urban nutrient input likely shapes the riverine microbial community. The families Actinomycetales F-ACK-M1, Rickettsiaceae, Betaproteobacteria O- SBla14 and Anaerolineae O-GCA004 demonstrated greatest network centrality, each interacting with seven first-neighbor taxa, suggesting an importance in community structure. Acetobacteraceae and Chloroflexi F-Dolo23 also exhibited network centrality and were directly linked to nitrate and nitrite, suggesting they play key roles in nitrogen cycling. Propionibacterium (44.82%) was the most dominant genera found in the Murray River followed by Anaerococcus (2.94%), and Finegoldia (2.05%). Comparison of the bacterial community comprising bio-floc and those found in the River Murray revealed that seven bacterial phyla including Proteobacteria, Bacteriodetes, Cyanobacteria, Actinobacteria, Planctomycetes, Verrumibrobia, and Chloroflexi common to bio-floc contributed to 95.8% total relative abundance in the river. However, based on genera level, there were14 bacteria genera in the river that generally present in bio-floc forming bacteria identified across all river samples constituted 4.63%. The potential bio-floc forming bacteria found mainly in downstream of the river provided various functions in the bio-floc system including producing natural flocculants to form microorganisms aggregates, a source of potential probiotics and prebiotics, nitrite oxidation and denitrification process, and degradation of organic matters.

The effect of the Yellow Sea Warm Current (YSWC) on virio- and bacterioplankton communities in the Bohai Sea is unknown. In this study, the composition and dynamic changes of virio- and bacterioplankton at the entrance of the Bohai Sea were measured to determine the influence of the YSWC on those communities and vice versa. In the Bohai Strait, there were east to west gradients of water chemistry and hydrology. The turbulent mixing between the deep north-western ‘warm’ current, which is 9°C, and the cold, nutrient-rich Bohai Sea water at 7–8°C appears to stimulate the abundance of both viruses and heterotrophic bacteria, with numbers at the junction of ‘warm’ and cold water being almost 10-fold greater than in the low-thermohaline areas, and peaking where the temperature is the highest. The average viral and bacterial abundances in the north-eastern area are much higher than in the south-western area. It proved that the YSWC entered the Bohai Sea with poor biomass and exited with rich biomass, which, in turn, enriches the Yellow Sea microbial loop. Our results showed the dramatic effect of temperature rise and increasing eutrophication on microbial abundance and marine microbial communities.

This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ which permits use, distribution and reproduction in any medium, provided the original work is properly cited. This author accepted manuscript is made available following 24 month embargo from date of publication (Sept 2018) in accordance with the publisher’s archiving policy, The Bohai Strait is a crucial pathway for water exchange between the Bohai Sea and the Yellow Sea, and exhibits a robust spatiotemporal pattern of hydrodynamic conditions. 16S rRNA amplicon sequencing was applied to study the spatiotemporal patterns of bacterial community composition and diversity in the Bohai Strait. Physical and chemical parameters were measured in order to explain what might control the observed patterns in community composition and diversity. In response to environmental changes between seasons, especially the dramatic changes of temperature and nutrient (NO2-N and PO4-P) levels, Synechococcus and unclassified genera in Family I predominated in summer while some oligotrophic taxa (e.g., Pelagibacter, OM43 clade) are more abundant in winter. The spatial heterogeneity and overall patchiness of bacterial assemblages in the Bohai Strait could not be well explained by the measured factors. However, the taxa with the most spatially variable presence and absence, e.g. Vibrionaceae, SAR11 and Sva0996 marine group, possess differentiated niches for utilization of organic matter (OM) and display a close relationship with the distribution of OM sources in this area, which may indicate the significance of OM sources to bacterial community structure. Our results suggest that local factors rather than regional factors, such as dispersal limited by hydrodynamics, structure the bacterial communities in the Bohai Strait., This work was supported by the National Basic Research Program (973 Program) of China (No. 2015CB453300), the External Cooperation Program of Chinese Academy of Sciences (No. 133337KYSB20180015), the Key Research Project of Frontier Science of Chinese Academy of Sciences (No. QYZDB-SSW-DQC041), the Strategic Priority Research Program of Chinese Academy of Sciences (No. XDA11020403), and the Technology Service Network Plan of Chinese Academy of Sciences (STS, No. ZSYS-006).

Groundwater is increasingly used globally for domestic, industrial and agricultural production. While many studies have focused on groundwater as a resource, the diverse ecosystems within are often ignored. Here, we assess 54 Southern South Australian groundwater microbial communities from the populated part of the state to assess their status and dynamics in isolated groundwater systems. We observed a strong site-to-site individuality in groundwater bacterial communities, likely due to the isolated nature of groundwater bodies leading to unique ecosystems. Rank abundance analysis indicates bacterial diversity is maintained even at low abundances and that the distribution fits classical ecological models for strong competition in resource-limited environments. Combined, our data indicates that despite overrepresentation of pollutant-associated bacterial orders in and around the Adelaide metropolitan area, microbial communities remain diverse and show little evidence of converging on a common pollutant-effected community.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited., The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur., This research was supported by a CSIRO Land and Water Top-Up PhD Scholarship (LD), a CSIRO consumables grant (LD), an APA to LD and Australian Research Council grants, www.arc.gov. au, LP-130100508 and DP-150103018 to JGM.

International audience; The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling;both are strongly infl uenced by human activities; including farming and extensive fl ow modifi cation.Metagenomic approaches were used to determine the planktonic bacterial community composition andpotential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-likesalinity, and the hypersaline upper-reaches of the estuary. Signifi cant shifts in taxa and metabolic functionwere seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceaeand Alteromonadaceae ; families readily able to adapt to change in nutrient conditions; and the potentiallypathogenic families Brucellaceae , Enterobacteriaceae and Vibrionaceae . Metabolisms over-representedinclude motility and chemotaxis, RNA metabolism and membrane transport, all of which are involvedin actively searching for and obtaining nutrients. Also over-represented were metabolisms involved inpopulation succession and stress response. An over-representation of taxa and metabolisms indicative ofenvironmental change is refl ective of anthropogenically aff ected riverine input. In the hypersaline upperreaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were thefamilies Flavobacteriaceae , Cytophagaceae and Nocardioidaceae , members of which are able to surviveover a wide salinity range. Metabolisms over-represented here were refl ective of increased bacterialgrowth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide andnucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically withother planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity,respectively. This indicates that the Coorong exhibits a unique planktonic bacterial community that isinfl uenced by riverine input at the river mouth and salinity in the upper-reaches.

Between 2004 and 2009, South Australia suffered its longest period of below average annual rainfall. This impacted riverine ecosystems and particularly the Murray-Darling Basin (MDB), the largest river system in Australia. The MDB combines 30,000 wetlands of which the Coorong wetland is of significant importance for the reproduction of bird and fish species, and is listed under the Ramsar Convention. We sampled water in the Coorong wetland between 2011 and 2013 and compiled additional data from 1997 to 2013 to assess the impact of the drought and subsequent recovery of the environment. The salinity levels of the Coorong wetland increased dramatically during the drought because of the lack of freshwater inflow from the Murray River. The changes in water flow observed from 2002 to 2009 had an impact on the number of habitats present along the Coorong wetland. In addition, a shift in community composition was observed between the freshwater habitat ( 85) dominated by diatoms. It is evident that during the drought, the Coorong wetland was dominated by diatoms and dinoflagellates. After the drought, the North Lagoon was dominated by chlorophytes up to a salinity level of 20. However, over 20 and in the South Lagoon, diatoms dominated the community. This study highlights how salinity levels drive the phytoplankton community. Based on the complementary data obtained for salinity between 1997 and 2010, there is a significant difference between the salinity levels observed during the drought and those observed before and after the drought. It appears that salinity levels are now recovered to what they were in the late 1990s.

Diatoms account for 25% of global primary productivity and are the base of many marine and freshwater food webs. They are encased in a porous silica matrix called a frustule, which within a species is reproduced exactly down to nanometres, but among species can be highly variable in terms of the morphology. The function of these nanometre structures is unknown. Diatoms are the most diverse unicellular microalgae with more than 100 000 known species. This diversity is reflected in and possibly caused by the porous outer silica coating known as the frustule. The frustule maintains cell shape, functions as a protective barrier, is a porous nutrient absorber, creates chemical nanoenvironments, provides structural defence against attackers and optically modifies impinging light fields. This wide variety of functions may explain the wide variety of nanostructures that permit the identification of so many tens of thousands of species with distinctive morphologies. However, to date there has been no review on the variety of structures. Here we present a review of the function of the diatom frustule and use the literature to highlight possible uses from understanding these functions. These structures offer the opportunity to understand how flow and chemical flux are modified at the nanoscale.

Carbon dioxide concentrating mechanisms (CCMs) act to improve the supply of CO2 at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase. There is substantial evidence that in some microalgal species CCMs involve an external carbonic anhydrase (CAext ) and that CAext activity is induced by low CO2 concentrations in the growth medium. However, much of this work has been conducted on cells adapted to air-equilibrium concentrations of CO2 , rather than to changing CO2 conditions caused by growing microalgal populations. We investigated the role of CAext in inorganic carbon (Ci ) acquisition and photosynthesis at three sampling points during the growth cycle of the cosmopolitan marine diatom Chaetoceros muelleri. We observed that CAext activity increased with decreasing Ci , particularly CO2 , concentration, supporting the idea that CAext is modulated by external CO2 concentration. Additionally, we found that the contribution of CAext activity to carbon acquisition for photosynthesis varies over time, increasing between the first and second sampling points before decreasing at the last sampling point, where external pH was high. Lastly, decreases in maximum quantum yield of photosystem II (Fv /Fm ), chlorophyll, maximum relative electron transport rate, light harvesting efficiency (α) and maximum rates of Ci - saturated photosynthesis (Vmax ) were observed over time. Despite this decrease in photosynthetic capacity an up-regulation of CCM activity, indicated by a decreasing half-saturation constant for CO2 (K0.5 CO2 ), occurred over time. The flexibility of the CCM during the course of growth in C. muelleri may contribute to the reported dominance and persistence of this species in phytoplankton blooms.

The muscle and liver fatty acid composition of young-of-the-year (YOY) Port Jackson sharks Heterodontus portusjacksoni were investigated to determine the effects of a known dietary lipid source v. maternal input as demonstrated by egg yolk fatty acid profiles. Ten Heterodontus portusjacksoni egg yolks were collected in situ and compared with four hatched H. portusjacksoni fed a known diet in a controlled feeding experiment of 185 days. This study demonstrated that fatty acids are probably conservatively transferred from egg yolks to YOY H. portusjacksoni, while diet did not have a large effect on the fatty acid composition of the liver or muscle.

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 10 11 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 × 10 6 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.

Six non-native deer species have established wild populations in Australia, and most are expanding in distribution and abundance. There is therefore increasing focus on the need to understand and manage these species. Capturing and immobilising wild deer is essential for many research and management applications, but the best methods for doing this have not been identified for the Australian situation. To address this knowledge gap, we systematically reviewed methods used to physically capture and chemically immobilise the six wild deer species in Australia. A variety of physical and chemical restraint methods have been used to capture wild deer in Australia, but these have seldom been reported in peer-reviewed publications. Physical capture methods have employed a variety of trapping and netting configurations. Some chemical immobilisation approaches have used oral baiting, but most have relied on darting of free-ranging animals or hand-injection of physically restrained deer. There is uncertainty about the efficacy and animal welfare impacts of the techniques currently used to capture wild deer in Australia. Improved reporting of capture outcomes would facilitate the identification of ‘best practice’ techniques for capturing wild deer in Australian environments.

Microbial electric systems (MESs) hold significant promise for the sustainable remediation of chlorinated solvents such as tetrachlorethene (perchloroethylene, PCE). Although the bio-electrochemical potential of some specific bacterial species such as Dehalcoccoides and Geobacteraceae have been exploited, this ability in other undefined microorganisms has not been extensively assessed. Hence, the focus of this study was to investigate indigenous and potentially bio-electrochemically active microorganisms in PCE-contaminated groundwater. Lab-scale MESs were fed with acetate and carbon electrode/PCE as electron donors and acceptors, respectively, under biostimulation (BS) and BS-bioaugmentation (BS-BA) regimes. Molecular analysis of the indigenous groundwater community identified mainly Spirochaetes, Firmicutes, Bacteroidetes, and γ and δ-Proteobacteria. Environmental scanning electron photomicrographs of the anode surfaces showed extensive indigenous microbial colonization under both regimes. This colonization and BS resulted in 100% dechlorination in both treatments with complete dechlorination occurring 4 weeks earlier in BS-BA samples and up to 11.5 μA of current being generated. The indigenous non-Dehalococcoides community was found to contribute significantly to electron transfer with ∼61% of the current generated due to their activities. This study therefore shows the potential of the indigenous non-Dehalococcoides bacterial community in bio-electrochemically reducing PCE that could prove to be a cost-effective and sustainable bioremediation practice.

Fatty acid (FA) analysis is increasingly being used as a tool to investigate the diet of sharks and rays. Quantifying the diet of sharks using FA profiles, however, requires an understanding of the effects that fluctuating diet has on the biochemical pathways in different tissues, and of the time scales of FA integration. The effects of dietary changes on the muscle and liver FA profiles were investigated in a controlled feeding experiment with Port Jackson sharks (Heterodontus portusjacksoni) fed exclusively on squid then prawns for six weeks each. Multivariate analysis indicated that shark muscle and liver FA profiles were 9.8% and 7.7% dissimilar after dietary change. This suggests that dietary FAs are preferentially utilised by muscle after dietary change and that muscle FA profiles are a stronger indicator of dietary changes occurring within three weeks of sampling than the FA profiles of the liver. This should be carefully considered when determining the type of tissue and frequency of sampling needed to undertake chondrichthyan dietary studies based on FA profile analysis. Some FA biomarkers and their metabolic processes are also identified and described, but further work is required to enable quantitative assessment of a species diet. Data presented here gives justification towards more complex experiments to investigate metabolic and FA tissue incorporation rates.