Diversity and Abundance of Club and Coral Fungi in the Upper Lane Cove Valley

The Kingdom Fungi are central players in the ecology and biogeochemistry of terrestrial ecosystems. Despite this importance, the diversity, distribution and abundance of fungal species are poorly known. Here, we undertook an intensive survey of club and coral fungi in the Upper Lane Cove Valley, Sydney, Australia. Over a two-year period, we collected more than 1100 specimens, and identified these to genus using a combination of DNA barcoding and morphology. The majority of specimens did not match any sequences in GenBank at more than 95% similarity, meaning that many of these fungi are either poorly represented in DNA databases, or are potentially novel species. A number of hotspots for fungal diversity and abundance were identified, largely along creek lines draining southwest through coachwood dominated vegetation. Notably, these hotspots all lie outside the adjacent Lane Cove National Park

Integrating biomedical, ecological, and sustainability sciences to manage emerging infectious diseases

Globalization accelerates the mobilization of microorganisms via international trade and transport. Growth in population, increasing connectivity, and rapid urbanization all exacerbate the consequent risk of pandemics of zoonotic diseases. Global problems require global solutions, particularly the co-ordination of international research in biomedical sciences, global ecology, and sustainability

Identification of the Rainbowfish in Lake Eacham Using DNA Sequencing

The Lake Eacham rainbowfish (Melanotaenia eachamensis) was once thought to be confined to its type locality within the Lake Eacham World Heritage National Park. M. eachamensis disappeared from the lake following the translocation of several species into the lake and the species was pronounced extinct in the wild in 1987. In a 2007 survey we noticed that rainbowfish were present in the lake once again. We used a molecular marker to identify these fish and the likely source population. Analysis of the D-loop region of mitochondrial DNA revealed that the species now present in the lake is Melanotaenia splendida, and is most closely related to several M. splendida populations in the immediate vicinity. Here we explore a range of scenarios that may have led to this colonisation event and highlight the dangers associated with translocation

Trophic level drives the host microbiome of soil invertebrates at a continental scale

Background: Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China. Results: Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web. Conclusions: Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates

Backreaction in Axion Monodromy, 4-forms and the Swampland

Axion monodromy models can always be described in terms of an axion coupled to 3-form gauge fields with non-canonical kinetic terms. The presence of the saxions parametrising the kinetic metrics of the 3-form fields leads to backreaction effects in the inflationary dynamics. We review the case in which saxions backreact on the K\"ahler metric of the inflaton leading to a logarithmic scaling of the proper field distance at large field. This behaviour is universal in Type II string flux compactifications and consistent with a refinement of the Swampland Conjecture. The critical point at which this behaviour appears depends on the mass hierarchy between the inflaton and the saxions. However, in tractable compactifications, such a hierarchy cannot be realised without leaving the regime of validity of the effective theory, disfavouring transplanckian excursions in string theory.Comment: Proceedings prepared for the "Workshop on Geometry and Physics", November 2016, Ringberg Castl

Test-retest reliability of spatial navigation in adults at-risk of Alzheimer’s disease

The Virtual Supermarket Task (VST) and Sea Hero Quest detect high-genetic-risk Alzheimer‘s disease (AD). We aimed to determine their test-retest reliability in a preclinical AD population. Over two time points, separated by an 18-month period, 59 cognitively healthy individuals underwent a neuropsychological and spatial navigation assessment. At baseline, participants were classified as low-genetic-risk of AD or high-genetic-risk of AD. We calculated two-way mixed effects intraclass correlation coefficients (ICC) for task parameters and used repeated measures ANOVAS to determine whether genetic risk or sex contributed to test-retest variability. The egocentric parameter of the VST measure showed the highest test–retest reliability (ICC = .72), followed by the SHQ distance travelled parameter (ICC = .50). Post hoc longitudinal analysis showed that boundary-based navigation predicts worsening episodic memory concerns in high-risk (F = 5.01, P = 0.03), but in not low-risk, AD candidates. The VST and the Sea Hero Quest produced parameters with acceptable test-retest reliability. Further research in larger sample sizes is desirable

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

BACKGROUND: Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. RESULTS: The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes). It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. CONCLUSION: Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phylogenetic distance separating two species and the rate at which they exchange gene cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio gene cassette pool as well as intragenomic translocation events of integrons in vibrios

Loss of soil microbial diversity exacerbates spread of antibiotic resistance

Loss of biodiversity is a major threat to the ecosystem processes upon which society depends. Natural ecosystems differ in their resistance to invasion by alien species, and this resistance can depend on the diversity in the system. Little is known, however, about the barriers that microbial diversity provides against microbial invasion. The increasing prevalence of antibiotic-resistant bacteria is a serious threat to public health in the 21st century. We explored the consequences of the reduction in soil microbial diversity for the dissemination of antibiotic resistance. The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR. Microbial diversity was negatively correlated with the abundance of antibiotic-resistance genes, and this correlation was maintained after accounting for other potential drivers such as incubation time and microbial abundance. Our results demonstrate that high microbial diversity can act as a biological barrier resist the spread of antibiotic resistance. These results fill a critical gap in our understanding of the role of soil microbial diversity in the health of ecosystem

Assessment of global health risk of antibiotic resistance genes

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health

The unusual occurrence of green algal balls of <i>Chaetomorpha linum</i> on a beach in Sydney, Australia.

In spring 2014, thousands of green algal balls were washed up at Dee Why Beach, Sydney, New South Wales, Australia. Reports of algal balls are uncommon in marine systems, and mass strandings on beaches are even more rare, sparking both public and scientific interest. We identified the algal masses as Chaetomorpha linum by using light microscopy and DNA sequencing. We characterize the size and composition of the balls from Dee Why Beach and compare them to previous records of marine algal balls. We describe the environmental conditions that could explain their appearance, given the ecophysiology of C. linum