CIE Spotlight: DNA amplification in the field: move over PCR, here comes LAMP

Patricia L.

Authors: Lee, Patricia L. M.

Source: MOLECULAR ECOLOGY RESOURCES, 17 (2):138-141, MAR 2017

Brief summary of the paper: It would not be an exaggeration to say that among molecular technologies, it is PCR (polymerase chain reaction) that underpins the discipline of molecular ecology as we know it today. With PCR, it has been possible to target the amplification of particular fragments of DNA, which can then be analysed in a multitude of ways.

The capability of PCR to amplify DNA from a mere handful of copies further means that conservationists and ecologists are able to sample DNA unobtrusively and with minimal disturbance to the environment and the organisms of interest. However, a key disadvantage of PCR-based methods has been the necessity for a generally non-portable, laboratory setting to undertake the time-consuming thermocycling protocols.

LAMP (loop-mediated isothermal amplification) offers a logistically simpler protocol: a relatively rapid DNA amplification reaction occurs at one temperature, and the products are visualized with a colour change within the reaction tubes. In the first field application of LAMP for an ecological study, Centeno-Cuadros et al. (2016) demonstrates how LAMP can be used to determine the sex of three raptor species. By enabling DNA amplification in situ and in ‘real-time’, LAMP promises to revolutionize how molecular ecology is practised in the field.

CIE Spotlight: Variability and Vulnerability of Coastal ‘Blue Carbon’ Stocks: A Case Study from Southeast Australia

Carolyn E., Paul C. and Peter M.

Authors: Carolyn J. Ewers Lewis, Paul E. Carnell, Jonathan Sanderman, Jeffrey A. Baldock, Peter I. Macreadie

Source: Frontiers in Ecology and the Environment, Volume 15, Issue 4, Pages 206–213, May 2017

Brief summary of the paper: ‘Blue carbon’ ecosystems—seagrasses, tidal marshes, and mangroves—serve as dense carbon sinks important for reducing atmospheric greenhouse gas concentrations, yet only recently have stock estimates emerged.

We sampled 96 blue carbon ecosystems across the Victorian coastline (southeast Australia) to quantify total sediment stocks, variability across spatial scales, and estimate emissions associated with historical ecosystem loss. Mean sediment organic carbon (Corg) stock (±SE) to a depth of 30 cm was not significantly different between tidal marshes (87.1 ± 4.90 Mg Corg ha−1) and mangroves (65.6 ± 4.17 Mg Corg ha−1), but was significantly lower in seagrasses (24.3 ± 1.82 Mg Corg ha−1). Location (defined as an individual meadow, marsh, or forest) had a stronger relationship with Corg stock than catchment region, suggesting local-scale conditions drive variability of stocks more than regional-scale processes.

We estimate over 2.90 million ± 199,000 Mg Corg in the top 30 cm of blue carbon sediments in Victoria (53% in tidal marshes, 36% in seagrasses, and 11% in mangroves) and sequestration rates of 22,700 ± 5510 Mg Corg year−1 (valued at over $AUD1 million ± 245,000 year−1 based on the average price of $AUD12.14 Mg CO2 eq−1 at Australian Emissions Reduction Fund auctions).

We estimate ecosystem loss since European settlement may equate to emissions as high as 4.83 million ± 358,000 Mg CO2 equivalents (assuming 90% remineralization of stocks), 98% of which was associated with tidal marsh loss, and what would have been sequestering 9360 ± 2500 Mg Corg year−1.

This study is among the first to present a comprehensive comparison of sediment stocks across and within coastal blue carbon ecosystems. We estimate substantial and valuable carbon stocks associated with these ecosystems that have suffered considerable losses in the past and need protection into the future to maintain their role as carbon sinks.

CIE Spotlight: Can we manage coastal ecosystems to sequester more blue carbon?

Peter M. and Stacey t. t.

Authors: Peter I Macreadie, Daniel A Nielsen, Jeffrey J Kelleway, Trisha B Atwood, Justin R Seymour, Katherina Petrou, Rod M Connolly, Alexandra CG Thomson, Stacey M Trevathan-Tackett, Peter J Ralph

Source: Frontiers in Ecology and the Environment, Volume 15, Issue 4, Pages 206–213, May 2017

Brief summary of the paper: To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches.

Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology.

By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.

CIE Spotlight: The global impacts of domestic dogs on threatened vertebrates

Tim D., Thomas N. and Euan R.

Authors: Tim S. Doherty, Chris R. Dickman, Alistair S. Glen, Thomas M. Newsome, Dale G. Nimmo, Euan G. Ritchie, Abi T. Vanak, Aaron J. Wirsing

Source: Biological Conservation, Volume 210, Part A, Pages 56–59, June 2017

Brief summary of the paper: Domestic dogs (Canis familiaris) have a near-global distribution. They range from being feral and free-ranging to owned and completely dependent on humans. All types of domestic dogs can interact with wildlife and have severe negative impacts on biodiversity.

Here, we use IUCN Red List data to quantify the number of threatened species negatively impacted by dogs, assess the prevalence of different types of dog impact, and identify regional hotspots containing high numbers of impacted species. Using this information, we highlight key research and management gaps and priorities.

Domestic dogs have contributed to 11 vertebrate extinctions and are a known or potential threat to at least 188 threatened species worldwide. These estimates are greater than those reported by previous assessments, but are probably conservative due to biases in the species, regions and types of impacts studied and/or reported. Predation is the most frequently reported impact, followed by disturbance, disease transmission, competition, and hybridisation. Regions with the most species impacted are: South-east Asia, Central America and the Caribbean, South America, Asia (excluding SE), Micro/Mela/Polynesia, and Australia.

We propose that the impacts of domestic dogs can be better understood and managed through: taxonomic and spatial prioritisation of research and management; examining potential synergisms between dogs and other threatening processes; strategic engagement with animal welfare and human health campaigns; community engagement and education; and mitigating anthropogenic effects such as resource subsidies.

Such actions are essential for threatened species persistence, especially given that human and dog populations are expected to increase both numerically and geographically in the coming decades.

CIE Seminar Series 2017 – The mind of plants: thinking the unthinkable

SPEAKER: Assoc. Prof. Monica Gagliano, Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, WA

DATE: Friday, 23rd June 2017
LOCATION: Geelong Campus at Waurn Ponds – room ka4.207
TIME: 1:30pm
Seminar will also be video linked to the following campuses: Melbourne Campus at Burwood – room T3.22; and Warrnambool Campus – room J2.22

External visitors – wish to join us and connect to our seminars?

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As a courtesy, we request that when connecting to the seminar that you mute your microphone unless you are required to speak, this would ensure that the sound from the speaker to the audience is not disrupted by feedback from your microphone – thank you!

ABSTRACT: Across all species, individuals thrive in complex ecological systems, which they rarely have complete knowledge of. To cope with this uncertainty and still make good choices while avoiding costly errors, organisms have developed the ability to exploit key features associated with their environment.

That through experience, humans and other animals are quick at learning to associate specific cues with particular places, events and circumstances has long been known; the idea that plants are also capable of learning by association had never been proven until now.

Here I comment on the recent paper that experimentally demonstrated associative learning in plants, thus qualifying them as proper subjects of cognitive research. Additionally, I make the point that the current fundamental premise in cognitive science, that we must understand the precise neural underpinning of a given cognitive feature in order to understand the evolution of cognition and behavior, needs to be re-imagined.

BIO: Monica Gagliano is a research associate professor of evolutionary ecology, an adjunct senior research fellow at the University of Western Australia and a former research fellow of the Australian Research Council.

She is the author of numerous scientific articles in the fields of animal and plant behavioral and evolutionary ecology and is co-editor of The Green Thread: Dialogues with the Vegetal World (Lexington, 2015) and The Language of Plants (Minnesota University Press, 2017).

She has pioneered the new research field of plant bioacoustics and extended the concept of cognition to plants, reigniting the discourse on plant subjectivity and ethical standing.

Appointments with guest speaker may be made via Jessica Hodgson.

CIE Spotlight: Effects of nutrient load on microbial activities within a seagrass-dominated ecosystem: Implications of changes in seagrass blue carbon

Peter M.

Authors: Liu, Songlin; Jiang, Zhijian; Wu, Yunchao; Zhang, Jingping; Arbi, Iman; Ye, Feng; Huang, Xiaoping; Macreadie, Peter Ian

Source: MARINE POLLUTION BULLETIN, 117 (1-2):214-221, APR 15 2017

Brief summary of the paper: Nutrient loading is a leading cause of global seagrass decline, triggering shifts from seagrass- to macroalgal-dominance. Within seagrass meadows of Xincun Bay (South China Sea), we found that nutrient loading (due to fish farming) increased sediment microbial biomass and extracellular enzyme activity associated with carbon cycling (polyphenol oxidase, invertase and cellulase), with a corresponding decrease in percent sediment organic carbon (SOC), suggesting that nutrients primed microorganism and stimulated SOC remineralization.

Surpisingly, however, the relative contribution of seagrass-derived carbon to bacteria (δ¹³Cbacteria) increased with nutrient loading, despite popular theory being that microbes switch to consuming macroalgae which are assumed to provide a more labile carbon source. Organic carbon sources of fungi were unaffected by nutrient loading.

Overall, this study suggests that nutrient loading changes the relative contribution of seagrass and algal sources to SOC pools, boosting sediment microbial biomass and extracellular enzyme activity, thereby possibly changing seagrass blue carbon.

CIE Spotlight: Proliferation of MISS-related microbial mats following the end-Permian mass extinction in the northern Paleo-Tethys: Evidence from southern Qilianshan region, western China

Guang S.

Authors: Xu, Yaling; Chen, Zhong-Qiang; Feng, Xueqian; Wu, Siqi; Shi, G. R.; Tu, Chenyi


Brief summary of the paper: As a consequence of the end-Permian mass extinction, microbes proliferated in the post-extinction shallow marine ecosystems, in which they grew as various microbially induced sedimentary structures (MISSs) in siliciclastic settings.

This paper reports, for the first time, the discovery of abundant MISSs from the lowest Triassic sandstones of shallow-water margin origin in the Zhihema sections of the southern Qilianshan region, West China. The sandstones are characterized by well-developed cross-beddings and ripple marks, and a Claraia-dominated bivalve assemblage of middle-late Griesbachian age. These sedimentary structures, together with the bivalves, suggest a high-energy peritidal zone of a shoreface setting in a clastic shallow sea environment.

Seven types of MISSs are recognized and described here: pictograph-like sand cracks/crack-fills, polygonal sand crack-fills, erosional remnants, multidirectional linear grooves, sinuous crack-fills, fusiform sand cracks/crack-fills, and leveled ripple marks. Most of the newly found MISSs are morphologically comparable with their ancient and modern counterparts. Detailed optical microscope and scanning electron microscope (SEM) analyses reveal that thin clayey laminae and filamentous mica grains are aligned parallel to bedding plane, and that the matrix-supported quartz grains, overall, are oriented; both of which are interpreted to indicate biogenic origin. The biogenic origin of these MISSs is reinforced by the presence of copious putative nanoglobules and filamentous biofilm-like organic objects in the interspaces of clay minerals in laminated layers.

These nanometer-scale objects are interpreted as bacterial bodies or remains that have been replaced with inorganic minerals upon fossilization. The presence of MISSs on the northern margins of Paleo-Tethys indicates that the post-extinction microbial mats had expanded their distributions from low-latitude to moderate-high latitude regions.

Moreover, unlike some previously reported microbial mats that contain very rare body and trace fossils, the southern Qilianshan MISSs were found in association with abundant vertical burrows and bivalves, suggesting that the MISS-forming microbial mats may have served as oases for trace-making organisms and opportunistic bivalves to flourish in shallow-marine habitats immediately after the end-Permian mass extinction.

CIE Spotlight: Variation in public perceptions and attitudes towards terrestrial ecosystems

Mike W.

Authors: Kiley, Heather M.; Ainsworth, Gillian B.; van Dongen, Wouter F. D.; Weston, Michael A.

Source: SCIENCE OF THE TOTAL ENVIRONMENT, 590 440-451, JUL 15 2017

Brief summary of the paper: Biodiversity is a global asset of inestimable value which is threatened by human activities. Biodiversity exists within ecosystems, which enjoy differing levels of conservation. The ways in which humans regard ecosystems can play an important role in identifying strategies to change human behaviour, thereby achieving conservation goals.

We investigated how preference, scenic attractiveness, perceptions of biodiversity and conservation value varied between five terrestrial ecosystems in Victoria, Australia (503 respondents). We document, for the first time, distinct ecosystem preferences, with people favouring wet forest, followed by dry forest, arid woodland/shrubland, heathland and then grassland.

The ecological worldview of the respondent (i.e., the set of beliefs that guide the way a person interacts with the natural world), their familiarity with the habitat and perceived scenic attractiveness influenced the conservation value assigned by the members of the public to each ecosystem. The conservation and biodiversity value assigned to each ecosystem was higher where people were familiar with the ecosystem, considered it attractive, and held an ecocentric worldview.

These aspects may correlate with public attitudes and represent key elements which could be used to engender higher levels of support for less appreciated ecosystems. Enhanced support may then underpin better conservation outcomes.

CIE Spotlight: Habitat selection by two sympatric rodent species in an alpine resort

Desley W.

Authors: Beilharz, Lisa V.; Whisson, Desley A.

Source: AUSTRALIAN JOURNAL OF ZOOLOGY, 64 (5):327-334 (Published online: 8 February 2017)

Brief summary of the paper: Conservation of small mammal species relies on an understanding of their habitat use.

We used trapping surveys and telemetry to examine habitat selection and use by the broad-toothed rat (Mastacomys fuscus mordicus) and the bush rat (Rattus fuscipes) in an alpine resort in Victoria. M. fuscus occurred at low numbers, nesting in subalpine wet heathland and foraging in that habitat as well as small patches of disturbed woodland.

In contrast, R. fuscipes was more common and nested in woodlands. Although foraging primarily in woodlands, R. fuscipes also foraged in all other available habitats. Both species showed strong selection for woodland fragments within ski runs.

Although highly disturbed, these habitats may provide important habitat and connectivity between less disturbed and larger habitat patches.

PhD Position @ UTAS: Learning to Live with Cancer – Local adaptations to transmissible tumours in Tasmanian devils

University of Tasmania is urgently looking for a PhD student to work on the diseases ecology and epidemiology of Tasmanian devil facial tumour disease.

The student will be based in Tasmania at the University of Tasmania, and will be supervised by Dr Rodrigo Hamede. The student will receive a 3 year PhD stipend, and if it’s an international student, then the offer comes with a tuition fee waiver, so no costs for the candidate.

They are looking for an outstanding candidate who is keen on doing fieldwork and ready to work with this iconic species.

Start date: As soon as possible.

For full details on this position CLICK HERE.

If you are or know a potential candidate, please pass on the details to her/him and ask the student to get in touch directly with Dr Rodrigo Hamede.