Managing for change: wetland transitions under sea‐level rise and outcomes for threatened species

Aim Global sea‐level rise (SLR) could be as much as 1.8 metres by 2100, which will impact coastal wetland communities and threatened species. We evaluated the likely outcomes of SLR for wetland communities using a process‐based simulation model and coupled this with a metapopulation model for a threatened native rodent (Xeromys myoides). Furthermore, we tested the amplified impacts of SLR, urban growth and introduced predators on X. myoides persistence. Location South‐east Queensland, Australia. Methods We adapted the Sea Level Affects Marshes Model to subtropical Australia. We used LiDAR elevation data, field data to parameterize surface accretion and shallow subsidence, and local knowledge to configure wetland transitions. SLR was simulated based on the IPCC B1 and A1FI scenarios, as well as the maximal limit of 1.8 m by 2100. Further, we coupled our demographic model to projected shifts in wetland habitat, and estimates of future wetland loss to urban expansion and feral cat (Felis catus) predation. Results Our models project a general decline in wetland communities under SLR, with a noted exception of mangroves. Under the A1FI scenario, SLR allows mangroves to migrate inland, with urban development acting as an obstruction in some areas. Mangrove expansion provides an unexpected benefit for dependent X. myoides populations, although the inclusion of predation and habitat loss due to urban development still suggests extirpation in c. 50 years. Main conclusions Through this case study, we illustrate the usefulness of process‐based SLR models in understanding outcomes for wetland communities and dependent species. Our models will underscore decision‐making in a dynamic system, with global applications for urban planning, conservation prioritization and wildlife management.     

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.     

A new leaf rust resistance gene <Emphasis Type="Italic">Lr79</Emphasis> mapped in chromosome 3BL from the durum wheat landrace Aus26582

Key message

A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection.

Abstract

Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3. LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2. LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708 and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3, only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3-linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79. Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels.

     

Protein kinase C{varepsilon} contributes to regulation of the sarcolemmal Na+-K+ pump

A reduction in angiotensinII (ANG II) in vivo by treatment of rabbits with theangiotensin-converting enzyme inhibitor, captopril, increasesNa⁺-K⁺ pump current (I_p)of cardiac myocytes. This increase is abolished by exposure of myocytesto ANG II in vitro. Because ANG II induces translocation of the-isoform of protein kinase C (PKC), we examined whether thisisozyme regulates the pump. We treated rabbits with captopril, isolatedmyocytes, and measured I_p of myocytes voltageclamped with wide-tipped patch pipettes. I_p ofmyocytes from captopril-treated rabbits was larger thanI_p of myocytes from controls. ANG II superfusionof myocytes from captopril-treated rabbits decreasedI_p to levels similar to controls. Inclusion ofPKC-specific blocking peptide in pipette solutions used to perfusethe intracellular compartment abolished the effect of ANG II. Inclusionof RACK, a PKC-specific activating peptide, in pipettesolutions had an effect on I_p that was similarto that of ANG II. There was no additive effect of ANG II andRACK. We conclude that PKC regulates the sarcolemmalNa⁺-K⁺ pump.

     

RGMIMS: a web-based Laboratory Information Management System for plant functional genomics research

A robust Laboratory Information Management System (LIMS) is required for the efficient handling of data generated from large-scale insertional mutagenesis projects. The Rice Gene Machine Information Management System (RGMIMS), a web-based modular LIMS, developed in a rice functional genomics laboratory at CSIRO, currently has four core modules: Seed Management, Transformation Management, Plant/Progeny Management, Phenotype Management, and an ad hoc querying module. RGMIMS manages, preserves and tracks large inventories of transgenic germplasm and enables efficient and accurate record keeping of the large quantities of experimental data. RGMIMS automates and seamlessly integrates multi-step experimental processes. A web user interface, incorporating barcoding utilities, enables rapid data capture and tracking of biological resources. Ontologies from Gramene and Plant Ontology consortium are used to describe mutant phenotypes. RGMIMS supports generic research processes in plant mutagenesis and could readily be adapted to general LIMS for high-throughput plant research.     

Temperature, air pollution and total mortality during summers in Sydney, 1994–2004

This study investigated the effect of temperature and air pollutants on total mortality in summers in Sydney, Australia. Daily data on weather variables, mortality and air pollution for the Sydney metropolitan area from 1 January 1994 to 31 December 2004 were supplied by Australian Bureau of Meteorology, Australian Bureau of Statistics, and Environment Protection Agency of New South Wales, respectively. We examined the association of total mortality with weather indicators and air pollution using generalised additive models (GAMs). A time-series classification and regression tree (CART) model was developed to explore the interaction effects of temperature and air pollution that impacted on mortality. Our results show that the average increase in total daily mortality was 0.9% [95% confidence interval (CI): 0.6-1.3%] and 22% (95% CI: 6.4-40.5%) for a 1 degrees C increase in daily maximum temperature and 1 part per hundred million (pphm) increase in daily average concentration of sulphur dioxide (SO(2)), respectively. Time-series CART results show that maximum temperature and SO(2) on the current day had significant interaction effects on total mortality. There were 7.3% and 12.1% increases in daily average mortality when maximum temperature was over 32 degrees C and mean SO(2) exceeded 0.315 pphm, respectively. Daily maximum temperature was statistically significantly associated with daily deaths in Sydney during summers between 1994 and 2004. Elevated daily maximum temperature combined with high SO(2) concentrations appeared to have contributed to the increased mortality observed in Sydney during this period.     

Conservation Research Is Not Happening Where It Is Most Needed

Target 19, set by the Convention on Biological Diversity, seeks to improve the knowledge, science base, and technologies relating to biodiversity. We will fail to achieve this target unless prolific biases in the field of conservation science are addressed. We reveal that comparatively less research is undertaken in the world’s most biodiverse countries, the science conducted in these countries is often not led by researchers based in-country, and these scientists are also underrepresented in important international fora. Mitigating these biases requires wide-ranging solutions: reforming open access publishing policies, enhancing science communication strategies, changing author attribution practices, improving representation in international processes, and strengthening infrastructure and human capacity for research in countries where it is most needed.In the environmental sciences, the scientific process generates evidence for policies and practices. Published evidence indicates that the quality standards associated with peer review have been met. Publishing also provides others with access to the evidence being shared, and increasingly, to the data and methodological processes underlying it. There are, however, strong biases in the peer-reviewed literature.Biodiversity and the threats to its persistence are not uniformly distributed across the globe and therefore some areas demand comparatively greater scientific attention. If research is biased away from the most biodiverse areas, then this will accentuate the impacts of the global biodiversity crisis and reduce our capacity to protect and manage the natural ecosystems that underpin human well-being. Target 19 of the Convention on Biodiversity (CBD) states that “By 2020, knowledge, the science base, and technologies relating to biodiversity, its values, functioning, status and trends, and the consequences of its loss, are improved, widely shared and transferred, and applied” [1]. Biases in conservation science will prevent us from achieving this target.We conducted the first comprehensive analysis of publishing trends of the conservation science literature. We identified all publications from 2014 on the topic of “conservation” in the research areas of environmental sciences, ecology, biodiversity conservation, plant sciences, zoology, and geography. We searched both the Thomson Reuters Zoological Records and Web of Science Core Collection databases, which returned 10,036 scientific publications (from 1,061 journals), after the duplicate, unrelated, and incomplete records were removed. For a subset of these publications (n = 7,593, or 81%), we manually identified at least one topic country, and we determined the relative conservation importance of these countries for mammal conservation [2] as well as a broader definition of conservation importance that considers richness of vascular plants, endemic species, and functional species [3].The countries for which knowledge is sparse coincide with where research is most urgently needed. The top five countries, ranked according to relative importance for mammal conservation (i.e, Indonesia, Madagascar, Peru, Mexico, and Australia), were represented in 11.9% of the publications (Fig 1). If we consider the broader definition of conservation importance that reflects the richness of vascular plants, endemic species, and functional species, then the top five countries (i.e., Ecuador, Costa Rica, Panama, the Dominican Republic, and Papua New Guinea) are the focus of only 1.6% of publications (4,5], will continue to be populated with biased data.Open in a separate windowFig 1Global distribution of publications on biodiversity conservation (S1 Data).

Table 1

Publishing trends and representation in the International Union for Conservation of Nature (IUCN) Specialist Groups or the Intergovernmental Panel on Biodiversity and Ecosystem Services (IPBES) for (A) the countries ranked highest in terms of importance for mammal conservation [2], (B) the countries ranked highest in terms of biodiversity [3], and (C) the United States and United Kingdom, for the purposes of comparison (S1 Data).

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single‐species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.     

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high‐coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single‐nucleotide polymorphisms (SNPs), of which 1 590 653 high‐confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype‐restricted, non‐synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near‐reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up‐CNVs), 112 630 genes present in fewer copies than in the reference genome (down‐CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland‐specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.