Publications by authors named "Suzanne M Prober"

42 Publications

Combating ecosystem collapse from the tropics to the Antarctic.

Glob Chang Biol 2021 05 25;27(9):1692-1703. Epub 2021 Feb 25.

School of Biological Sciences, Monash University, Clayton, Vic., Australia.

Globally, collapse of ecosystems-potentially irreversible change to ecosystem structure, composition and function-imperils biodiversity, human health and well-being. We examine the current state and recent trajectories of 19 ecosystems, spanning 58° of latitude across 7.7 M km , from Australia's coral reefs to terrestrial Antarctica. Pressures from global climate change and regional human impacts, occurring as chronic 'presses' and/or acute 'pulses', drive ecosystem collapse. Ecosystem responses to 5-17 pressures were categorised as four collapse profiles-abrupt, smooth, stepped and fluctuating. The manifestation of widespread ecosystem collapse is a stark warning of the necessity to take action. We present a three-step assessment and management framework (3As Pathway Awareness, Anticipation and Action) to aid strategic and effective mitigation to alleviate further degradation to help secure our future.
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http://dx.doi.org/10.1111/gcb.15539DOI Listing
May 2021

Increasing effects of chronic nutrient enrichment on plant diversity loss and ecosystem productivity over time.

Ecology 2021 02 18;102(2):e03218. Epub 2021 Jan 18.

Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA.

Human activities are enriching many of Earth's ecosystems with biologically limiting mineral nutrients such as nitrogen (N) and phosphorus (P). In grasslands, this enrichment generally reduces plant diversity and increases productivity. The widely demonstrated positive effect of diversity on productivity suggests a potential negative feedback, whereby nutrient-induced declines in diversity reduce the initial gains in productivity arising from nutrient enrichment. In addition, plant productivity and diversity can be inhibited by accumulations of dead biomass, which may be altered by nutrient enrichment. Over longer time frames, nutrient addition may increase soil fertility by increasing soil organic matter and nutrient pools. We examined the effects of 5-11 yr of nutrient addition at 47 grasslands in 12 countries. Nutrient enrichment increased aboveground live biomass and reduced plant diversity at nearly all sites, and these effects became stronger over time. We did not find evidence that nutrient-induced losses of diversity reduced the positive effects of nutrients on biomass; however, nutrient effects on live biomass increased more slowly at sites where litter was also increasing, regardless of plant diversity. This work suggests that short-term experiments may underestimate the long-term nutrient enrichment effects on global grassland ecosystems.
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http://dx.doi.org/10.1002/ecy.3218DOI Listing
February 2021

Global impacts of fertilization and herbivore removal on soil net nitrogen mineralization are modulated by local climate and soil properties.

Glob Chang Biol 2020 Dec 22;26(12):7173-7185. Epub 2020 Sep 22.

Grupo de Investigaciones en Biología de la Conservación, INIBIOMA (CONICET-UNCOMA), Bariloche, Argentina.

Soil nitrogen (N) availability is critical for grassland functioning. However, human activities have increased the supply of biologically limiting nutrients, and changed the density and identity of mammalian herbivores. These anthropogenic changes may alter net soil N mineralization (soil net N ), that is, the net balance between N mineralization and immobilization, which could severely impact grassland structure and functioning. Yet, to date, little is known about how fertilization and herbivore removal individually, or jointly, affect soil net N across a wide range of grasslands that vary in soil and climatic properties. Here we collected data from 22 grasslands on five continents, all part of a globally replicated experiment, to assess how fertilization and herbivore removal affected potential (laboratory-based) and realized (field-based) soil net N . Herbivore removal in the absence of fertilization did not alter potential and realized soil net N . However, fertilization alone and in combination with herbivore removal consistently increased potential soil net N Realized soil net N , in contrast, significantly decreased in fertilized plots where herbivores were removed. Treatment effects on potential and realized soil net N were contingent on site-specific soil and climatic properties. Fertilization effects on potential soil net N were larger at sites with higher mean annual precipitation (MAP) and temperature of the wettest quarter (T.q.wet). Reciprocally, realized soil net N declined most strongly with fertilization and herbivore removal at sites with lower MAP and higher T.q.wet. In summary, our findings show that anthropogenic nutrient enrichment, herbivore exclusion and alterations in future climatic conditions can negatively impact soil net N across global grasslands under realistic field conditions. This is an important context-dependent knowledge for grassland management worldwide.
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http://dx.doi.org/10.1111/gcb.15308DOI Listing
December 2020

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data.

Sci Data 2020 07 9;7(1):225. Epub 2020 Jul 9.

Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, 38010, Italy.

The FLUXNET2015 dataset provides ecosystem-scale data on CO, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.
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http://dx.doi.org/10.1038/s41597-020-0534-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347557PMC
July 2020

Microbial processing of plant remains is co-limited by multiple nutrients in global grasslands.

Glob Chang Biol 2020 08 10;26(8):4572-4582. Epub 2020 Jun 10.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.

Microbial processing of aggregate-unprotected organic matter inputs is key for soil fertility, long-term ecosystem carbon and nutrient sequestration and sustainable agriculture. We investigated the effects of adding multiple nutrients (nitrogen, phosphorus and potassium plus nine essential macro- and micro-nutrients) on decomposition and biochemical transformation of standard plant materials buried in 21 grasslands from four continents. Addition of multiple nutrients weakly but consistently increased decomposition and biochemical transformation of plant remains during the peak-season, concurrent with changes in microbial exoenzymatic activity. Higher mean annual precipitation and lower mean annual temperature were the main climatic drivers of higher decomposition rates, while biochemical transformation of plant remains was negatively related to temperature of the wettest quarter. Nutrients enhanced decomposition most at cool, high rainfall sites, indicating that in a warmer and drier future fertilized grassland soils will have an even more limited potential for microbial processing of plant remains.
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http://dx.doi.org/10.1111/gcb.15146DOI Listing
August 2020

Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands.

Glob Chang Biol 2020 Feb 3. Epub 2020 Feb 3.

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.

Grasslands are subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations and the climate. Here, we use the Nutrient Network experiment to examine the responses of soil C and N pools to mammalian herbivore exclusion across 22 grasslands, under ambient and elevated nutrient availabilities (fertilized with NPK + micronutrients). We show that the impact of herbivore exclusion on soil C and N pools depends on fertilization. Under ambient nutrient conditions, we observed no effect of herbivore exclusion, but under elevated nutrient supply, pools are smaller upon herbivore exclusion. The highest mean soil C and N pools were found in grazed and fertilized plots. The decrease in soil C and N upon herbivore exclusion in combination with fertilization correlated with a decrease in aboveground plant biomass and microbial activity, indicating a reduced storage of organic matter and microbial residues as soil C and N. The response of soil C and N pools to herbivore exclusion was contingent on temperature - herbivores likely cause losses of C and N in colder sites and increases in warmer sites. Additionally, grasslands that contain mammalian herbivores have the potential to sequester more N under increased temperature variability and nutrient enrichment than ungrazed grasslands. Our study highlights the importance of conserving mammalian herbivore populations in grasslands worldwide. We need to incorporate local-scale herbivory, and its interaction with nutrient enrichment and climate, within global-scale models to better predict land-atmosphere interactions under future climate change.
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http://dx.doi.org/10.1111/gcb.15023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155038PMC
February 2020

Recent climate-driven ecological change across a continent as perceived through local ecological knowledge.

PLoS One 2019 22;14(11):e0224625. Epub 2019 Nov 22.

Department of the Environment and Energy, Canberra, Australian Capital Territory, Australia.

Documenting effects of climate change is an important step towards designing mitigation and adaptation responses. Impacts of climate change on terrestrial biodiversity and ecosystems have been well-documented in the Northern Hemisphere, but long-term data to detect change in the Southern Hemisphere are limited, and some types of change are generally difficult to measure. Here we present a novel approach using local ecological knowledge to facilitate a continent-scale view of climate change impacts on terrestrial biodiversity and ecosystems that people have perceived in Australia. We sought local knowledge using a national web-based survey, targeting respondents with close links to the environment (e.g. farmers, ecologists), and using a custom-built mapping tool to ask respondents to describe and attribute recent changes they had observed within an area they knew well. Results drawn from 326 respondents showed that people are already perceiving simple and complex climate change impacts on hundreds of species and ecosystems across Australia, significantly extending the detail previously reported for the continent. While most perceived trends and attributions remain unsubstantiated, >35 reported anecdotes concurred with examples in the literature, and >20 were reported more than once. More generally, anecdotes were compatible with expectations from global climate change impact frameworks, including examples across the spectrum from organisms (e.g. increased mortality in >75 species), populations (e.g. changes in recruitment or abundance in >100 species, phenological change in >50 species), and species (e.g. >80 species newly arriving or disappearing), to communities and landscapes (e.g. >50 examples of altered ecological interactions). The overarching pattern indicated by the anecdotes suggests that people are more often noticing climate change losers (typically native species) than winners in their local areas, but with observations of potential 'adaptation in action' via compositional and phenological change and through arrivals and range shifts (particularly for native birds and exotic plants). A high proportion of climate change-related anecdotes also involved cumulative or interactive effects of land use. We conclude that targeted elicitation of local ecological knowledge about climate change impacts can provide a valuable complement to data-derived knowledge, substantially extending the volume of explicit examples and offering a foundation for further investigation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224625PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874335PMC
April 2020

How well do revegetation plantings capture genetic diversity?

Biol Lett 2019 10 16;15(10):20190460. Epub 2019 Oct 16.

Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3052, Australia.

Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic diversity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global literature comparing genetic diversity in revegetation plantings to natural stands. Findings from 48 studies suggest variable genetic outcomes of revegetation, with 46% demonstrating higher genetic diversity in revegetation than natural stands and 52% demonstrating lower diversity. Levels of genetic diversity were most strongly associated with the number of source sites used-where information was available, 69% of studies showing higher genetic diversity in revegetation reported using multiple provenances, compared with only 33% for those with lower diversity. However, with a few exceptions, it was unclear whether differences in genetic diversity between revegetation and natural stands were statistically significant. This reflected insufficient reporting of statistical error and metadata within the published studies, which limited conclusions about factors contributing to patterns. Nonetheless, our findings indicate that mixed seed sourcing can contribute to higher genetic diversity in revegetation. Finally, we emphasize the type of metadata needed to determine factors influencing genetic diversity in revegetation and inform restoration efforts.
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http://dx.doi.org/10.1098/rsbl.2019.0460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832181PMC
October 2019

Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient.

Ecol Lett 2019 Dec 14;22(12):2077-2086. Epub 2019 Oct 14.

Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.

A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.
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http://dx.doi.org/10.1111/ele.13389DOI Listing
December 2019

Fire-mediated habitat change regulates woodland bird species and functional group occurrence.

Ecol Appl 2019 12 27;29(8):e01997. Epub 2019 Sep 27.

Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia.

In an era characterized by recurrent large wildfires in many parts of the globe, there is a critical need to understand how animal species respond to fires, the rates at which populations can recover, and the functional changes fires may cause. Using quantified changes in habitat parameters over a ~400-yr post-fire chronosequence in an obligate-seeding Australian eucalypt woodland, we build and test predictions of how birds, as individual species and aggregated into functional groups according to their use of specific habitat resources, respond to time since fire. Individual bird species exhibited four generalized response types to time since fire: incline, decline, delayed, and bell. All significant relationships between bird functional group richness or abundance and time since fire were consistent with predictions based on known time-since-fire-associated changes in habitat features putatively important for these bird groups. Consequently, we argue that the bird community is responding to post-fire successional changes in habitat as per the habitat accommodation model, rather than to time since fire per se, and that our functional framework will be of value in predicting bird responses to future disturbances in this and other obligate-seeder forest and woodland ecosystems. Most bird species and functional groups that were affected by time since fire were associated with long-unburned woodlands. In the context of recent large, stand-replacement wildfires that have affected a substantial proportion of obligate-seeder eucalypt woodlands, and the multi-century timescales over which post-fire succession occurs, it would appear preferable from a bird conservation perspective if fires initiating loss of currently long-unburned woodlands were minimized. Once long-unburned woodlands are transformed by fire into recently burned woodlands, there is limited scope for alternative management interventions to accelerate the rate of habitat development after fire, or supplement the resources formerly provided to birds by long-unburned woodlands, with the limited exception of augmenting hollow availability for key hollow-nesting species.
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http://dx.doi.org/10.1002/eap.1997DOI Listing
December 2019

Phylogenomics shows lignotuber state is taxonomically informative in closely related eucalypts.

Mol Phylogenet Evol 2019 06 23;135:236-248. Epub 2019 Mar 23.

Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia. Electronic address:

Plant taxa can be broadly divided based on the mechanisms enabling persistence through whole-crown disturbances, specifically whether individuals resprout, populations reseed, or both or neither of these mechanisms are employed. At scales from species through to communities, the balance of disturbance-response types has major ramifications for ecological function and biodiversity conservation. In some lineages, morphologically identical populations except for differences in a disturbance-response trait (e.g. ± lignotuber) occur, offering the opportunity to apply genetic analyses to test whether trait state is representative of broader genetic distinctiveness, or alternatively, variation in response to local environmental conditions. In eucalypts, a globally-significant plant group, we apply dense taxon sampling and high-density, genome-wide markers to test monophyly and genetic divergence among pairs of essentially morphologically-identical taxa excepting lignotuber state. Taxa differing in lignotuber state formed discrete phylogenetic lineages. Obligate-seeders were monophyletic and strongly differentiated from each other and lignotuber-resprouters, but this was not the case for all lignotuber-resprouter taxa. One lignotuber state transition within our sample clade was supported, implying convergence of some non-lignotuber morphology characters. Greater evolutionary rate associated with the obligate-seeder disturbance-response strategy offers a plausible explanation for these genetic patterns. Lignotuber state is an important taxonomic character in eucalypts, with transitions in lignotuber state having contributed to the evolution of the exceptional diversity of eucalypts in south-western Australia. Differences in lignotuber state have evolved directionally with respect to environmental conditions.
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http://dx.doi.org/10.1016/j.ympev.2019.03.016DOI Listing
June 2019

Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs.

Nat Ecol Evol 2019 03 4;3(3):400-406. Epub 2019 Feb 4.

Forest Research Centre, School of Agriculture, University of Lisbon, Lisbon, Portugal.

Leaf traits are frequently measured in ecology to provide a 'common currency' for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)-a commonly measured morphological trait inferring shifts between plant growth strategies-did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus and potassium concentrations increased in response to the addition of each respective soil nutrient. We found few significant changes in leaf traits when vertebrate herbivores were excluded in the short-term. Leaf nitrogen and potassium concentrations were positively correlated with species turnover, suggesting that interspecific trait variation was a significant predictor of leaf nitrogen and potassium, but not of leaf phosphorus concentration. Climatic conditions and pretreatment soil nutrient levels also accounted for significant amounts of variation in the leaf traits measured. Overall, we find that leaf morphological traits, such as specific leaf area, are not appropriate indicators of plant response to anthropogenic perturbations in grasslands.
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http://dx.doi.org/10.1038/s41559-018-0790-1DOI Listing
March 2019

Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient.

Ecology 2018 04 31;99(4):822-831. Epub 2018 Mar 31.

Department of Ecology, Evolution, and Behavior, University of MN, St. Paul, Minnesota, 55108, USA.

Plant stoichiometry, the relative concentration of elements, is a key regulator of ecosystem functioning and is also being altered by human activities. In this paper we sought to understand the global drivers of plant stoichiometry and compare the relative contribution of climatic vs. anthropogenic effects. We addressed this goal by measuring plant elemental (C, N, P and K) responses to eutrophication and vertebrate herbivore exclusion at eighteen sites on six continents. Across sites, climate and atmospheric N deposition emerged as strong predictors of plot-level tissue nutrients, mediated by biomass and plant chemistry. Within sites, fertilization increased total plant nutrient pools, but results were contingent on soil fertility and the proportion of grass biomass relative to other functional types. Total plant nutrient pools diverged strongly in response to herbivore exclusion when fertilized; responses were largest in ungrazed plots at low rainfall, whereas herbivore grazing dampened the plant community nutrient responses to fertilization. Our study highlights (1) the importance of climate in determining plant nutrient concentrations mediated through effects on plant biomass, (2) that eutrophication affects grassland nutrient pools via both soil and atmospheric pathways and (3) that interactions among soils, herbivores and eutrophication drive plant nutrient responses at small scales, especially at water-limited sites.
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http://dx.doi.org/10.1002/ecy.2175DOI Listing
April 2018

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.

Nat Ecol Evol 2018 Jan 4;2(1):50-56. Epub 2017 Dec 4.

Department of Plant & Soil Sciences, University of Kentucky, Lexington, KY, 40546-0091, USA.

Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.
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http://dx.doi.org/10.1038/s41559-017-0395-0DOI Listing
January 2018

Linear infrastructure impacts on landscape hydrology.

J Environ Manage 2018 Jan 7;206:446-457. Epub 2017 Dec 7.

School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, Perth, WA, 6009, Australia.

The extent of roads and other forms of linear infrastructure is burgeoning worldwide, but their impacts are inadequately understood and thus poorly mitigated. Previous studies have identified many potential impacts, including alterations to the hydrological functions and soil processes upon which ecosystems depend. However, these impacts have seldom been quantified at a regional level, particularly in arid and semi-arid systems where the gap in knowledge is the greatest, and impacts potentially the most severe. To explore the effects of extensive track, road, and rail networks on surface hydrology at a regional level we assessed over 1000 km of linear infrastructure, including approx. 300 locations where ephemeral streams crossed linear infrastructure, in the largely intact landscapes of Australia's Great Western Woodlands. We found a high level of association between linear infrastructure and altered surface hydrology, with erosion and pooling 5 and 6 times as likely to occur on-road than off-road on average (1.06 erosional and 0.69 pooling features km on vehicle tracks, compared with 0.22 and 0.12 km, off-road, respectively). Erosion severity was greater in the presence of tracks, and 98% of crossings of ephemeral streamlines showed some evidence of impact on water movement (flow impedance (62%); diversion of flows (73%); flow concentration (76%); and/or channel initiation (31%)). Infrastructure type, pastoral land use, culvert presence, soil clay content and erodibility, mean annual rainfall, rainfall erosivity, topography and bare soil cover influenced the frequency and severity of these impacts. We conclude that linear infrastructure frequently affects ephemeral stream flows and intercepts natural overland and near-surface flows, artificially changing site-scale moisture regimes, with some parts of the landscape becoming abnormally wet and other parts becoming water-starved. In addition, linear infrastructure frequently triggers or exacerbates erosion, leading to soil loss and degradation. Where linear infrastructure densities are high, their impacts on ecological processes are likely to be considerable. Linear infrastructure is widespread across much of this relatively intact region, but there remain areas with very low infrastructure densities that need to be protected from further impacts. There is substantial scope for mitigating the impacts of existing and planned infrastructure developments.
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http://dx.doi.org/10.1016/j.jenvman.2017.10.036DOI Listing
January 2018

Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change.

Mol Ecol 2017 Nov 7;26(21):6002-6020. Epub 2017 Oct 7.

CSIRO Land and Water, Floreat, WA, Australia.

Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long-lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of F outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty-one SNPs were identified as putatively adaptive, based on significance in F outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species' evolutionary potential.
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http://dx.doi.org/10.1111/mec.14341DOI Listing
November 2017

Bioclimatic transect networks: Powerful observatories of ecological change.

Ecol Evol 2017 07 19;7(13):4607-4619. Epub 2017 May 19.

Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.

Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost-effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population- and community-level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate-induced changes, which will inform effective management actions for promoting biodiversity resilience.
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http://dx.doi.org/10.1002/ece3.2995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496522PMC
July 2017

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.

Genome Biol Evol 2017 02;9(2):253-265

Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia.

Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
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http://dx.doi.org/10.1093/gbe/evw290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381606PMC
February 2017

Symbiosis limits establishment of legumes outside their native range at a global scale.

Nat Commun 2017 04 7;8:14790. Epub 2017 Apr 7.

CSIRO Agriculture and Food, Canberra, Clunies Ross Street, Acton, Australian Capital Territory 2601, Australia.

Microbial symbiosis is integral to plant growth and reproduction, but its contribution to global patterns of plant distribution is unknown. Legumes (Fabaceae) are a diverse and widely distributed plant family largely dependent on symbiosis with nitrogen-fixing rhizobia, which are acquired from soil after germination. This dependency is predicted to limit establishment in new geographic areas, owing to a disruption of compatible host-symbiont associations. Here we compare non-native establishment patterns of symbiotic and non-symbiotic legumes across over 3,500 species, covering multiple independent gains and losses of rhizobial symbiosis. We find that symbiotic legume species have spread to fewer non-native regions compared to non-symbiotic legumes, providing strong support for the hypothesis that lack of suitable symbionts or environmental conditions required for effective nitrogen-fixation are driving these global introduction patterns. These results highlight the importance of mutualisms in predicting non-native species establishment and the potential impacts of microbial biogeography on global plant distributions.
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http://dx.doi.org/10.1038/ncomms14790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385628PMC
April 2017

Addition of multiple limiting resources reduces grassland diversity.

Nature 2016 09 24;537(7618):93-96. Epub 2016 Aug 24.

Swiss Federal Institute for Forest, Snow and Landscape Research, Community Ecology, Birmensdorf 8903, Switzerland.

Niche dimensionality provides a general theoretical explanation for biodiversity-more niches, defined by more limiting factors, allow for more ways that species can coexist. Because plant species compete for the same set of limiting resources, theory predicts that addition of a limiting resource eliminates potential trade-offs, reducing the number of species that can coexist. Multiple nutrient limitation of plant production is common and therefore fertilization may reduce diversity by reducing the number or dimensionality of belowground limiting factors. At the same time, nutrient addition, by increasing biomass, should ultimately shift competition from belowground nutrients towards a one-dimensional competitive trade-off for light. Here we show that plant species diversity decreased when a greater number of limiting nutrients were added across 45 grassland sites from a multi-continent experimental network. The number of added nutrients predicted diversity loss, even after controlling for effects of plant biomass, and even where biomass production was not nutrient-limited. We found that elevated resource supply reduced niche dimensionality and diversity and increased both productivity and compositional turnover. Our results point to the importance of understanding dimensionality in ecological systems that are undergoing diversity loss in response to multiple global change factors.
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http://dx.doi.org/10.1038/nature19324DOI Listing
September 2016

Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box).

New Phytol 2016 Dec 21;212(4):992-1006. Epub 2016 Jul 21.

Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Rd, Parkville, Vic, 3010, Australia.

In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.
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http://dx.doi.org/10.1111/nph.14084DOI Listing
December 2016

The Australian SuperSite Network: A continental, long-term terrestrial ecosystem observatory.

Sci Total Environ 2016 Oct 3;568:1263-1274. Epub 2016 Jun 3.

Forestry Tasmania, Hobart, Australia.

Ecosystem monitoring networks aim to collect data on physical, chemical and biological systems and their interactions that shape the biosphere. Here we introduce the Australian SuperSite Network that, along with complementary facilities of Australia's Terrestrial Ecosystem Research Network (TERN), delivers field infrastructure and diverse, ecosystem-related datasets for use by researchers, educators and policy makers. The SuperSite Network uses infrastructure replicated across research sites in different biomes, to allow comparisons across ecosystems and improve scalability of findings to regional, continental and global scales. This conforms with the approaches of other ecosystem monitoring networks such as Critical Zone Observatories, the U.S. National Ecological Observatory Network; Analysis and Experimentation on Ecosystems, Europe; Chinese Ecosystem Research Network; International Long Term Ecological Research network and the United States Long Term Ecological Research Network. The Australian SuperSite Network currently involves 10 SuperSites across a diverse range of biomes, including tropical rainforest, grassland and savanna; wet and dry sclerophyll forest and woodland; and semi-arid grassland, woodland and savanna. The focus of the SuperSite Network is on using vegetation, faunal and biophysical monitoring to develop a process-based understanding of ecosystem function and change in Australian biomes; and to link this with data streams provided by the series of flux towers across the network. The Australian SuperSite Network is also intended to support a range of auxiliary researchers who contribute to the growing body of knowledge within and across the SuperSite Network, public outreach and education to promote environmental awareness and the role of ecosystem monitoring in the management of Australian environments.
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http://dx.doi.org/10.1016/j.scitotenv.2016.05.170DOI Listing
October 2016

Comment on "Worldwide evidence of a unimodal relationship between productivity and plant species richness".

Science 2016 Jan;351(6272):457

Department of Ecology, Environment and Evolution, La Trobe University, Kingsbury Drive, Bundoora 3086, Victoria, Australia.

Fraser et al. (Reports, 17 July 2015, p. 302) report a unimodal relationship between productivity and species richness at regional and global scales, which they contrast with the results of Adler et al. (Reports, 23 September 2011, p. 1750). However, both data sets, when analyzed correctly, show clearly and consistently that productivity is a poor predictor of local species richness.
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http://dx.doi.org/10.1126/science.aad6236DOI Listing
January 2016

Integrative modelling reveals mechanisms linking productivity and plant species richness.

Nature 2016 Jan 13;529(7586):390-3. Epub 2016 Jan 13.

Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, Colorado 80526, USA.

How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.
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http://dx.doi.org/10.1038/nature16524DOI Listing
January 2016

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe.

Proc Natl Acad Sci U S A 2015 Sep 17;112(35):10967-72. Epub 2015 Aug 17.

Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309;

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.
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http://dx.doi.org/10.1073/pnas.1508382112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568213PMC
September 2015

Plant species' origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands.

Nat Commun 2015 Jul 15;6:7710. Epub 2015 Jul 15.

Department of Entomology, University of Maryland, College Park Maryland 20742, USA.

Exotic species dominate many communities; however the functional significance of species' biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.
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http://dx.doi.org/10.1038/ncomms8710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518311PMC
July 2015

Grassland productivity limited by multiple nutrients.

Nat Plants 2015 Jul 6;1:15080. Epub 2015 Jul 6.

Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, USA.

Terrestrial ecosystem productivity is widely accepted to be nutrient limited(1). Although nitrogen (N) is deemed a key determinant of aboveground net primary production (ANPP)(2,3), the prevalence of co-limitation by N and phosphorus (P) is increasingly recognized(4-8). However, the extent to which terrestrial productivity is co-limited by nutrients other than N and P has remained unclear. Here, we report results from a standardized factorial nutrient addition experiment, in which we added N, P and potassium (K) combined with a selection of micronutrients (K+μ), alone or in concert, to 42 grassland sites spanning five continents, and monitored ANPP. Nutrient availability limited productivity at 31 of the 42 grassland sites. And pairwise combinations of N, P, and K+μ co-limited ANPP at 29 of the sites. Nitrogen limitation peaked in cool, high latitude sites. Our findings highlight the importance of less studied nutrients, such as K and micronutrients, for grassland productivity, and point to significant variations in the type and degree of nutrient limitation. We suggest that multiple-nutrient constraints must be considered when assessing the ecosystem-scale consequences of nutrient enrichment.
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http://dx.doi.org/10.1038/nplants.2015.80DOI Listing
July 2015

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide.

Ecol Lett 2015 Jan 28;18(1):85-95. Epub 2014 Nov 28.

CSIRO Land and Water Flagship, Private Bag 5, Wembley, WA, 6913, Australia.

Aboveground-belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m(2) plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.
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http://dx.doi.org/10.1111/ele.12381DOI Listing
January 2015