Environmental factors controlling soil respiration in three semiarid ecosystems

Previous research suggests that soil organic C pools may be a feature of semiarid regions that are particularly sensitive to climatic changes. We instituted an 18-mo experiment along an elevation gradient in northern Arizona to evaluate the influence of temperature, moisture, and soil C pool size on soil respiration. Soils, from underneath different free canopy types and interspaces of three semiarid ecosystems, were moved upslope and/or downslope to modify soil climate. Soils moved downslope experienced increased temperature and decreased precipitation, resulting in decreased soil moisture and soil respiration las much as 23 acid 20%, respectively). Soils moved upslope to more mesic, cooler sites had greater soil water content and increased rates of soil respiration las much as 40%), despite decreased temperature. Soil respiration rates normalized for total C were not significantly different within any of the three incubation sites, indicating that under identical climatic conditions, soil respiration is directly related to soil C pool size for the incubated soils. Normalized soil respiration rates between sites differed significantly for all soil types and were always greater for soils incubated under more mesic, but cooler, conditions. Total soil C did not change significantly during the experiment, but estimates suggest that significant portions of the rapidly cycling C pool were lost. While long-term decreases in aboveground and belowground detrital inputs may ultimately be greater than decreased soil respiration, the initial response to increased temperature and decreased precipitation in these systems is a decrease in annual soil C efflux.

The urban littoral frontier : land reclamation in the history of human settlements

The urban waterfront may be regarded as the littoral frontier of human settlement. Typically, over the years, it advances, sometimes retreats, where terrestrial and aquatic processes interact and frequently contest this margin of occupation. Because most towns and cities are sited beside water bodies, many of these urban centers on or close to the sea, their physical expansion is constrained by the existence of aquatic areas in one or more directions from the core. It is usually much easier for new urban development to occur along or inland from the waterfront. Where other physical constraints, such as rugged hills or mountains, make expansion difficult or expensive, building at greater densities or construction on steep slopes is a common response. This kind of development, though technically feasible, is usually more expensive than construction on level or gently sloping land, however. Moreover, there are many reasons for developing along the shore or riverfront in preference to using sites further inland. The high cost of developing existing dry land that presents serious construction difficulties is one reason for creating new land from adjacent areas that are permanently or periodically under water. Another reason is the relatively high value of artificially created land close to the urban centre when compared with the value of existing developable space at a greater distance inland. The creation of space for development is not the only motivation for urban expansion into aquatic areas. Commonly, urban places on the margins of the sea, estuaries, rivers or great lakes are, or were once, ports where shipping played an important role in the economy. The demand for deep waterfronts to allow ships to berth and for adjacent space to accommodate various port facilities has encouraged the advance of the urban land area across marginal shallows in ports around the world. The space and locational demands of port related industry and commerce, too, have contributed to this process. Often closely related to these developments is the generation of waste, including domestic refuse, unwanted industrial by-products, site formation and demolition debris and harbor dredgings. From ancient times, the foreshore has been used as a disposal area for waste from nearby settlements, a practice that continues on a huge scale today. Land formed in this way has long been used for urban development, despite problems that can arise from the nature of the dumped material and the way in which it is deposited. Disposal of waste material is a major factor in the creation of new urban land. Pollution of the foreshore and other water margin wetlands in this way encouraged the idea that the reclamation of these areas may be desirable on public health grounds. With reference to examples from various parts of the world, the historical development of the urban littoral frontier and its effects on the morphology and character of towns and cities are illustrated and discussed. The threat of rising sea levels and the heritage value of many waterfront areas are other considerations that are addressed.

Solving navigational uncertainty using grid cells on robots

To successfully navigate their habitats, many mammals use a combination of two mechanisms, path integration and calibration using landmarks, which together enable them to estimate their location and orientation, or pose. In large natural environments, both these mechanisms are characterized by uncertainty: the path integration process is subject to the accumulation of error, while landmark calibration is limited by perceptual ambiguity. It remains unclear how animals form coherent spatial representations in the presence of such uncertainty. Navigation research using robots has determined that uncertainty can be effectively addressed by maintaining multiple probabilistic estimates of a robot's pose. Here we show how conjunctive grid cells in dorsocaudal medial entorhinal cortex (dMEC) may maintain multiple estimates of pose using a brain-based robot navigation system known as RatSLAM. Based both on rodent spatially-responsive cells and functional engineering principles, the cells at the core of the RatSLAM computational model have similar characteristics to rodent grid cells, which we demonstrate by replicating the seminal Moser experiments. We apply the RatSLAM model to a new experimental paradigm designed to examine the responses of a robot or animal in the presence of perceptual ambiguity. Our computational approach enables us to observe short-term population coding of multiple location hypotheses, a phenomenon which would not be easily observable in rodent recordings. We present behavioral and neural evidence demonstrating that the conjunctive grid cells maintain and propagate multiple estimates of pose, enabling the correct pose estimate to be resolved over time even without uniquely identifying cues. While recent research has focused on the grid-like firing characteristics, accuracy and representational capacity of grid cells, our results identify a possible critical and unique role for conjunctive grid cells in filtering sensory uncertainty. We anticipate our study to be a starting point for animal experiments that test navigation in perceptually ambiguous environments.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Engineering an Ecosystem : Taking Cues from Nature’s Paradigm to Build Tissue in the Lab and the Body

This manuscript took a 'top down' approach to understanding survival of inhabitant cells in the ecosystem bone, working from higher to lower length and time scales through the hierarchical ecosystem of bone. Our working hypothesis is that nature “engineered” the skeleton using a 'bottom up' approach,where mechanical properties of cells emerge from their adaptation to their local me-chanical milieu. Cell aggregation and formation of higher order anisotropic struc- ture results in emergent architectures through cell differentiation and extracellular matrix secretion. These emergent properties, including mechanical properties and architecture, result in mechanical adaptation at length scales and longer time scales which are most relevant for the survival of the vertebrate organism [Knothe Tate and von Recum 2009]. We are currently using insights from this approach to har-ness nature’s regeneration potential and to engineer novel mechanoactive materials [Knothe Tate et al. 2007, Knothe Tate et al. 2009]. In addition to potential applications of these exciting insights, these studies may provide important clues to evolution and development of vertebrate animals. For instance, one might ask why mesenchymal stem cells condense at all? There is a putative advantage to self-assembly and cooperation, but this advantage is somewhat outweighed by the need for infrastructural complexity (e.g., circulatory systems comprised of specific differentiated cell types which in turn form conduits and pumps to overcome limitations of mass transport via diffusion, for example; dif-fusion is untenable for multicellular organisms larger than 250 microns in diameter. A better question might be: Why do cells build skeletal tissue? Once cooperatingcells in tissues begin to deplete local sources of food in their aquatic environment, those that have evolved a means to locomote likely have an evolutionary advantage. Once the environment becomes less aquarian and more terrestrial, self-assembled organisms with the ability to move on land might have conferred evolutionary ad-vantages as well. So did the cytoskeleton evolve several length scales, enabling the emergence of skeletal architecture for vertebrate animals? Did the evolutionary advantage of motility over noncompliant terrestrial substrates (walking on land) favor adaptations including emergence of intracellular architecture (changes in the cytoskeleton and upregulation of structural protein manufacture), inter-cellular con- densation, mineralization of tissues, and emergence of higher order architectures?How far does evolutionary Darwinism extend and how can we exploit this knowl- edge to engineer smart materials and architectures on Earth and new, exploratory environments?[Knothe Tate et al. 2008]. We are limited only by our ability to imagine. Ultimately, we aim to understand nature, mimic nature, guide nature and/or exploit nature’s engineering paradigms without engineer-ing ourselves out of existence.

Design and implementation of sensor networks for the observation and research of harmful algal blooms in southern California coastal waters

Harmful Algal Blooms (HABs) have become an important environmental concern along the western coast of the United States. Toxic and noxious blooms adversely impact the economies of coastal communities in the region, pose risks to human health, and cause mortality events that have resulted in the deaths of thousands of fish, marine mammals and seabirds. One goal of field-based research efforts on this topic is the development of predictive models of HABs that would enable rapid response, mitigation and ultimately prevention of these events. In turn, these objectives are predicated on understanding the environmental conditions that stimulate these transient phenomena. An embedded sensor network (Fig. 1), under development in the San Pedro Shelf region off the Southern California coast, is providing tools for acquiring chemical, physical and biological data at high temporal and spatial resolution to help document the emergence and persistence of HAB events, supporting the design and testing of predictive models, and providing contextual information for experimental studies designed to reveal the environmental conditions promoting HABs. The sensor platforms contained within this network include pier-based sensor arrays, ocean moorings, HF radar stations, along with mobile sensor nodes in the form of surface and subsurface autonomous vehicles. FreewaveTM radio modems facilitate network communication and form a minimally-intrusive, wireless communication infrastructure throughout the Southern California coastal region, allowing rapid and cost-effective data transfer. An emerging focus of this project is the incorporation of a predictive ocean model that assimilates near-real time, in situ data from deployed Autonomous Underwater Vehicles (AUVs). The model then assimilates the data to increase the skill of both nowcasts and forecasts, thus providing insight into bloom initiation as well as the movement of blooms or other oceanic features of interest (e.g., thermoclines, fronts, river discharge, etc.). From these predictions, deployed mobile sensors can be tasked to track a designated feature. This focus has led to the creation of a technology chain in which algorithms are being implemented for the innovative trajectory design for AUVs. Such intelligent mission planning is required to maneuver a vehicle to precise depths and locations that are the sites of active blooms, or physical/chemical features that might be sources of bloom initiation or persistence. The embedded network yields high-resolution, temporal and spatial measurements of pertinent environmental parameters and resulting biology (see Fig. 1). Supplementing this with ocean current information and remotely sensed imagery and meteorological data, we obtain a comprehensive foundation for developing a fundamental understanding of HAB events. This then directs labor- intensive and costly sampling efforts and analyses. Additionally, we provide coastal municipalities, managers and state agencies with detailed information to aid their efforts in providing responsible environmental stewardship of their coastal waters.

Can hybridization cause local extinction : the case for demographic swamping of the Australian native, Senecio pinnatifolius, by the invasive, S. madagascariensis?

The outcome of interspecific hybridization between native and invasive species depends on the relative frequencies of parental taxa and viability of hybrid progeny. We investigated individual and population level consequences of hybridization between the Australian native, Senecio pinnatifolius, and the exotic S. madagascariensis, with AFLP markers and used this information to simulate the expected outcome of hybridization.A high frequency (range 8.3-75.6 %) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations indicating that sympatric populations represent tension zones. A hybridization advantage was observed for S. madagascariensis,where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Simulations indicated S. pinnatifolius could be replaced in sympatric populations if hybridization was density dependent.For this native-exotic pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. Due to asymmetric hybridization, S. pinnatifolius appears under threat from demographic swamping, and local extinction is possible where it occurs in sympatry with S. madagascariensis.

Ecology and behavior of first instar larval Lepidoptera

Neonate Lepidoptera are confronted with the daunting task of establishing themselves on a food plant. The factors relevant to this process need to be considered at spatial and temporal scales relevant to the larva and not the investigator. Neonates have to cope with an array of plant surface characters as well as internal characters once the integument is ruptured. These characters, as well as microclimatic conditions, vary within and between plant modules and interact with larval feeding requirements, strongly affecting movement behavior, which may be extensive even for such small organisms. In addition to these factors, there is an array of predators, pathogens, and parasitoids with which first instars must contend. Not surprisingly, mortality in neonates is high but can vary widely. Experimental and manipulative studies, as well as detailed observations of the animal, are vital if the subtle interaction of factors responsible for this high and variable mortality are to be understood. These studies are essential for an understanding of theories linking female oviposition behavior with larval survival, plant defense theory, and population dynamics, as well as modern crop resistance breeding programs.

Management of a tributyl tin issue in a marina development in Queensland

Tributyl tin (TBT) deposits in the sediments are one of many impacts that have been imposed on both the environment and the up-coming development of Boat Haven, Airlie Beach, Queensland. The current costly solution to this problem (that is, removal and re-burial) could be put in future to the credit of the developer rather than be treated (as at present) as a penalty. The Queensland Government’s Offsets Scheme provides an opportunity to promote effective conservation of regional landscapes. Because this scheme plans for offsetting in terrestrial vegetation systems through rehabilitation, so credits could be given to those approved developers who rehabilitate valuable marine habitats disturbed by TBT deposits.

Par4 is a coactivator for a splice isoform-specific transcriptional activation domain in WT1

The Wilms’ tumor suppressor protein WT1 is a transcriptional regulator involved in differentiation and the regulation of cell growth. WT1 is subject to alternative splicing, one isoform including a 17–amino acid region that is specific to mammals. The function of this 17–amino acid insertion is not clear, however. Here, we describe a transcriptional activation domain in WT1 that is specific to the WT1 splice isoform that contains the 17–amino acid insertion. We show that the function of this domain in transcriptional activation is dependent on a specific interaction with the prostate apoptosis response factor par4. A mutation in WT1 found in Wilms’ tumor disturbs the interaction with par4 and disrupts the function of the activation domain. Analysis of WT1 derivatives in cells treated to induce par4 expression showed a strong correlation between the transcription function of the WT1 17–amino acid insertion and the ability of WT1 to regulate cell survival and proliferation. Our results provide a molecular mechanism by which alternative splicing of WT1 can regulate cell growth in development and disease.

Improved design method for biosecurity surveillance and early detection of non-indigenous rats

A recent advance in biosecurity surveillance design aims to benefit island conservation through early and improved detection of incursions by non-indigenous species. The novel aspects of the design are that it achieves a specified power of detection in a cost-managed system, while acknowledging heterogeneity of risk in the study area and stratifying the area to target surveillance deployment. The design also utilises a variety of surveillance system components, such as formal scientific surveys, trapping methods, and incidental sightings by non-biologist observers. These advances in design were applied to black rats (Rattus rattus) representing the group of invasive rats including R. norvegicus, and R. exulans, which are potential threats to Barrow Island, Australia, a high value conservation nature reserve where a proposed liquefied natural gas development is a potential source of incursions. Rats are important to consider as they are prevalent invaders worldwide, difficult to detect early when present in low numbers, and able to spread and establish relatively quickly after arrival. The ‘exemplar’ design for the black rat is then applied in a manner that enables the detection of a range of non-indigenous species of rat that could potentially be introduced. Many of the design decisions were based on expert opinion as data gaps exist in empirical data. The surveillance system was able to take into account factors such as collateral effects on native species, the availability of limited resources on an offshore island, financial costs, demands on expertise and other logistical constraints. We demonstrate the flexibility and robustness of the surveillance system and discuss how it could be updated as empirical data are collected to supplement expert opinion and provide a basis for adaptive management. Overall, the surveillance system promotes an efficient use of resources while providing defined power to detect early rat incursions, translating to reduced environmental, resourcing and financial costs.

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the advantage of cheaper and increased sampling but make available so much data that automated analysis becomes essential. The report describes a number of tools for automated analysis of recordings, including noise removal from spectrograms, acoustic event detection, event pattern recognition, spectral peak tracking, syntactic pattern recognition applied to call syllables, and oscillation detection. These algorithms are applied to a number of animal call recognition tasks, chosen because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are frequent contaminants of recordings of the terrestrial environment; (2) the detection of bird and calls; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4-5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

Barrow Island's biosecurity : catching the unknown invader

When industry meets a conservation area, animals or plants from outside may hitch a lift and potentially wreak havoc. How can you be sure of catching the intruders – or at least 80% sure? A government directive instructed Frith Jarrad, Peter Whittle, Susan Barrett and Kerrie Mengersen to come up with a statistically measurable scheme.

Prioritizing land and sea conservation investments to protect coral reefs

Background: Coral reefs have exceptional biodiversity, support the livelihoods of millions of people, and are threatened by multiple human activities on land (e.g. farming) and in the sea (e.g. overfishing). Most conservation efforts occur at local scales and, when effective, can increase the resilience of coral reefs to global threats such as climate change (e.g. warming water and ocean acidification). Limited resources for conservation require that we efficiently prioritize where and how to best sustain coral reef ecosystems.----- ----- Methodology/Principal Findings: Here we develop the first prioritization approach that can guide regional-scale conservation investments in land-and sea-based conservation actions that cost-effectively mitigate threats to coral reefs, and apply it to the Coral Triangle, an area of significant global attention and funding. Using information on threats to marine ecosystems, effectiveness of management actions at abating threats, and the management and opportunity costs of actions, we calculate the rate of return on investment in two conservation actions in sixteen ecoregions. We discover that marine conservation almost always trumps terrestrial conservation within any ecoregion, but terrestrial conservation in one ecoregion can be a better investment than marine conservation in another. We show how these results could be used to allocate a limited budget for conservation and compare them to priorities based on individual criteria.----- ----- Conclusions/Significance: Previous prioritization approaches do not consider both land and sea-based threats or the socioeconomic costs of conserving coral reefs. A simple and transparent approach like ours is essential to support effective coral reef conservation decisions in a large and diverse region like the Coral Triangle, but can be applied at any scale and to other marine ecosystems.