Research Outputs (Animal, Plant and Environmental Sciences)

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    A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
    (Public Library of Science, 2018-03) Geldenhuys, M.; Mortlock, M.; Weyer, J.; Bezuidt, O.; Seamark, E.C.J; Kearney, T.
    Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.
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    Carnivore conservation needs evidence based livestock protection
    (Public Library of Science, 2018-09) van Eeden, L.M.; Eklund, A.; Miller, J.R.B.; López-Bao, J.V; Chapron, G.; Cejtin, M.R.; McManus, J.
    Carnivore predation on livestock often leads people to retaliate. Persecution by humans has contributed strongly to global endangerment of carnivores. Preventing livestock losses would help to achieve three goals common to many human societies: preserve nature, protect animal welfare, and safeguard human livelihoods. Between 2016 and 2018, four independent reviews evaluated >40 years of research on lethal and nonlethal interventions for reducing predation on livestock. From 114 studies, we find a striking conclusion: scarce quantitative comparisons of interventions and scarce comparisons against experimental controls preclude strong inference about the effectiveness of methods. For wise investment of public resources in protecting livestock and carnivores, evidence of effectiveness should be a prerequisite to policy making or large-scale funding of any method or, at a minimum, should be measured during implementation. An appropriate evidence base is needed, and we recommend a coalition of scientists and managers be formed to establish and encourage use of consistent standards in future experimental evaluations.
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    Chiefs in a Democracy: A Case Study of the 'New' Systems of Regulating Firewood Harvesting in Post-Apartheid South Africa
    (MDPI, 2018-03) Findlay, S.J.; Twine, W.C.
    Much of the international commons literature reveals a decreased functioning of local traditional institutions that regulate natural resource harvesting. In South Africa, it is believed that the creation of new democratic structures at the end of Apartheid has contributed significantly to the deterioration in traditional resource regulation and this in turn has led to the extensive resource degradation seen in parts of the country. Many of these assertions, though, remain anecdotal in nature. Given the high reliance by rural households on natural resources, and the serious negative implications that over-use has on livelihood security, understanding how well or poorly such commons are regulated is key to ensuring the sustainability of such resource-dependent populations. The aim of this study was therefore to examine systems of resource governance, focusing specifically on firewood, and to determine the roles of traditional and democratically elected community leaders in six rural villages spanning two chieftaincies in Bushbuckridge, South Africa. In each study village, five local leaders were interviewed and five community focus groups were conducted. Results indicate that most parties still regard the Chief as the ultimate authority for regulating firewood harvesting. However, overall firewood management appears weak, at best, across the region. Although some authors attribute this to community confusion over the roles of local leaders in a new democracy, we provide evidence that other socio-political factors, including political expediency, may be driving the increasingly relaxed implementation of these firewood management systems. With resource dependence remaining a vital contributor to livelihood security across the developing world and with many rural communities facing increasing strain under local resource depletion, these findings shed new light on the complex social dynamics underlying the widely reported weakening of traditional institutions in South Africa. In so doing, it offers insights into local firewood governance that can be used to combat these challenges and thereby reduce regional social and ecological vulnerability being experienced in communal landscapes across the region.
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    Transplant Experiments Point to Fire Regime as Limiting Savanna Tree Distribution
    (Frontiers Media, 2018-09-18) Stevens, N.; Archibald, S.; Bond, W.J.
    Plant species range shifts are predicted to occur in response to climate change. The predictions are often based on the assumption that climate is the primary factor limiting the distribution of species. However the distribution of grassy biomes in Africa cannot be predicted by climate alone, instead interactions between vegetation, climate and disturbance structure the ecosystems. To test if climatic variables, as predicted by an environmental niche model, determine the distribution limits of two common savanna tree species we established a transplant experiment at a range of latitudes and altitudes much broader than the distribution limits of our study species. We planted seedlings of two common savanna trees, Senegalia nigrescens and Colophospermum mopane, at eight paired high and low elevation sites across an 850 km latitudinal gradient in South African savannas. At each site seedlings were planted in both grassy and cleared plots. After 2 years of growth, rainfall, temperature and location inside or outside their distribution range did not explain species success. Grass competition was the only variable that significantly affected plant growth rates across all sites, but grass competition alone could not explain the distribution limit. Species distributions were best predicted when maximum tree growth rates were considered in relation to local fire return intervals. The probability of sapling escape from the fire trap was the most likely determinant of distribution limits of these two species. As trees grew and survived 100 s of kilometers south of their current range limits we conclude that climate alone does not explain the current distribution of these trees, and that climate change adaptation strategies for savanna environments based only on climatic envelope modeling will be inappropriate.
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    Biological and geophysical feedbacks with fire in the Earth system
    (Environmental Research Letters, 2018-03-06) Archibald, S.; Lehmann, C.E.R.; Belcher, C.M.; Bond, W.J.; Bradstock, R.A.
    Roughly 3% of the Earth's land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels-namely plants and their litter-that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences.
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    Geology drives the spatial patterning and structure of termite mounds in an African savanna
    (Ecosphere, 2018-03) Muvengwi, J.; Davies, A.B.; Parrini, F.; Witkowski, E.T.F.
    Termite mounds perform important roles in savanna ecosystems, generating heterogeneity and influencing ecosystem processes across multiple trophic levels. However, the influence the environment and neighboring termite colonies have on mound spatial patterning and structure is poorly understood, despite the profound implications such dynamics can have on ecosystems. To better understand these drivers, we mapped the spatial distribution and size of active and inactive Macrotermes mounds in eight 1-km2 plots on contrasting geologies, nutrient-rich granite and nutrient-poor basalt, in a semi-arid Zimbabwean savanna. Although mound density was not significantly different between basalt (5.5 mounds/ha) and granite (6.1 mounds/ha), termite mound structural attributes and spatial distribution patterns varied greatly between geologies. Mound size distributions differed between the geologies and mounds were 2.6 times taller and 3.9 times wider and had 15 times greater lateral surface area on granite. Subsequently, 6% of the total landscape was covered by mounds on granite compared with only 0.4% on basalt. On granite, large mounds exhibited significant over-dispersion at scales below 30 m, signifying density-dependent thinning. Furthermore, small mounds were clustered around large mounds, likely a result of the budding of new colonies comprising fully fledged castes less vulnerable to competition. In contrast, random patterning was evident on comparably homogenous basalt. Our results demonstrate the powerful influence geological substrate has on mound spatial patterning and structure, suggesting that the importance of termite mounds for ecosystem functioning is more pronounced on nutrient-poor granitic substrates than basalts because of the pronounced over-dispersion, which maximizes mound production per unit area, and much larger mound sizes here.
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    Vegetation type conservation targets, status and level of protection in KwaZulu-Natal in 2016
    (AOSIS (pty) Ltd, 2018-05-09) Jewitt, D.
    Background: Systematic conservation planning aims to ensure representivity and persistence of biodiversity. Quantitative targets set to meet these aims provide a yardstick with which to measure the current conservation status of biodiversity features and measure the success of conservation actions. Objectives: The conservation targets and current ecosystem status of vegetation types and biomes occurring in KwaZulu-Natal (KZN) were assessed, and their level of formal protection was determined, to inform conservation planning initiatives in the province. Method: Land cover maps of the province were used to determine the amount of natural habitat remaining in KZN. This was intersected with the vegetation map and assessed relative to their conservation targets to determine the ecosystem status of each vegetation type in KZN. The proclaimed protected areas were used to determine the level of protection of each vegetation type. Results: In 17 years (1994-2011), 19.7% of natural habitat was lost to anthropogenic conversion of the landscape. The Indian Ocean Coastal Belt and Grassland biomes had the least remaining natural habitat, the highest rates of habitat loss and the least degree of formal protection. Conclusion: These findings inform conservation priorities in the province. Vegetation type targets need to be revised to ensure long-term persistence. Business-as-usual is no longer an option if we are to meet the legislative requirements and mandates to conserve the environment for current and future generations.
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    The consequences of replacing wildlife with livestock in Africa
    (Scientific Reports, 2017-12-01) Hempson, G.P.; Archibald, S.; Bond, W.J.
    The extirpation of native wildlife species and widespread establishment of livestock farming has dramatically distorted large mammal herbivore communities across the globe. Ecological theory suggests that these shifts in the form and the intensity of herbivory have had substantial impacts on a range of ecosystem processes, but for most ecosystems it is impossible to quantify these changes accurately. We address these challenges using species-level biomass data from sub-Saharan Africa for both present day and reconstructed historical herbivore communities. Our analyses reveal pronounced herbivore biomass losses in wetter areas and substantial biomass increases and functional type turnover in arid regions. Fire prevalence is likely to have been altered over vast areas where grazer biomass has transitioned to above or below the threshold at which grass fuel reduction can suppress fire. Overall, shifts in the functional composition of herbivore communities promote an expansion of woody cover. Total herbivore methane emissions have more than doubled, but lateral nutrient diffusion capacity is below 5% of past levels. The release of fundamental ecological constraints on herbivore communities in arid regions appears to pose greater threats to ecosystem function than do biomass losses in mesic regions, where fire remains the major consumer.
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    Comparative studies need to rely both on sound natural history data and on excellent statistical analysis
    (Royal Society Publishing, 2017-09-20) Schradin, C.
    No abstract available
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    Carbon lost and carbon gained: a study of vegetation and carbon trade-offs among diverse land uses in Phoenix, Arizona
    (Ecological Society of America, 2017-03-01) Hall, S.J.; Majumdar, A.; McHale, M.R.; Grimm, N.B.
    Human modification and management of urban landscapes drastically alters vegetation and soils, thereby altering carbon (C) storage and rates of net primary productivity (NPP). Complex social and ecological processes drive vegetation cover in cities, leading to heterogeneity in C dynamics depending on regional climate, land use, and land cover. Recent work has demonstrated homogenization in ecological processes within human-dominated landscapes (the urban convergence hypothesis) in soils and biotic communities. However, a lack of information on vegetation in arid land cities has hindered an understanding of potential C storage and NPP convergence across a diversity of ecosystem types. We estimated C storage and NPP of trees and shrubs for six different land-use types in the arid metropolis of Phoenix, Arizona, USA, and compared those results to native desert ecosystems, as well as other urban and natural systems around the world. Results from Phoenix do not support the convergence hypothesis. In particular, C storage in urban trees and shrubs was 42% of that found in desert vegetation, while NPP was only 20% of the total NPP estimated for comparable natural ecosystems. Furthermore, the overall estimates of C storage and NPP associated with urban trees in the CAP ecosystem were much lower (8-63%) than the other cities included in this analysis. We also found that C storage (175.25-388.94 g/m2) and NPP (8.07-15.99 g·m-2·yr-1) were dominated by trees in the urban residential land uses, while in the desert, shrubs were the primary source for pools (183.65 g/m2) and fluxes (6.51 g·m-2·yr-1). These results indicate a trade-off between shrubs and trees in arid ecosystems, with shrubs playing a major role in overall C storage and NPP in deserts and trees serving as the dominant C pool in cities. Our research supports current literature that calls for the development of spatially explicit and standardized methods for analyzing C dynamics associated with vegetation in urbanizing areas.
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    Variation by Geographic Scale in the Migration-Environment Association: Evidence from Rural South Africa
    (Federal Institute for Population Research, 2017) Hunter, L.M.; Leyk, S.; Maclaurin, G.J.; Nawrotzki, R.; Twine, W.; Erasmus, B.F.N.; Collinson, M.
    Scholarly understanding of human migration’s environmental dimensions has greatly advanced in the past several years, motivated in large part by public and policy dialogue around “climate migrants”. The research presented here advances current demographic scholarship both through its substantive interpretations and conclusions, as well as its methodological approach. We examine temporary rural South African outmigration as related to household-level availability of proximate natural resources. Such “natural capital” is central to livelihoods in the region, both for sustenance and as materials for market-bound products. The results demonstrate that the association between local environmental resource availability and outmigration is, in general, positive: households with higher levels of proximate natural capital are more likely to engage in temporary migration. In this way, the general findings support the “environmental surplus” hypothesis that resource security provides a foundation from which households can invest in migration as a livelihood strategy. Such insight stands in contrast to popular dialogue, which tends to view migration as a last resort undertaken only by the most vulnerable households. As another important insight, our findings demonstrate important spatial variation, complicating attempts to generalize migration-environment findings across spatial scales. In our rural South African study site, the positive association between migration and proximate resources is actually highly localized, varying from strongly positive in some villages to strongly negative in others. We explore the socio-demographic factors underlying this “operational scale sensitivity”. The cross-scale methodologies applied here offer nuance unavailable within more commonly used global regression models, although also introducing complexity that complicates story-telling and inhibits generalizability.
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    Notes on the flowering and pollination of the endemic grassland Aloe reitzii var. reitzii (Asphodelaceae)
    (AOSIS (pty) Ltd, 2017) Symes, C.T.
    Aloe reitzii var. reitzii is a succulent with a restricted distribution in the montane grassland of eastern South Africa. It is a summer (late January-March) flowering succulent that grows on rocky outcrops at 1000 m-1600 m, and the conspicuous inflorescences suggest a pollination system focused towards birds. Objectives: To understand more about the pollination biology of A. reitzii var. reitzii. Methods: Nectar standing crop (flower volume and concentration) and the proportion of plants flowering were recorded. Camera traps and observations were used to record visitors to A. reitzii var. reitzii inflorescences. Results: Nectar volume was 36 μL ± 27 μL per flower (range 6 μL-93 μL; n = 27) and concentration was 16.5% ± 1.7% (range 13.5% - 19.5%). Camera trap observations, where 18.9% of all plants were observed flowering, recorded the three bird species Cape Weaver, Ploceus capensis, Malachite Sunbird, Nectarinia famosa and Greater Double-collared Sunbird, Cinnyris afer (60.4%, 27.1% and 12.5% of plant visits, respectively) visiting inflorescences. Conclusion: Because birds are important pollinators for many Aloe species, it is assumed that the bird species detected visiting A. reitzii var. reitzii are similarly important pollinators. At least 10 invertebrate species and sengi (Elephantulus sp.) were also recorded as visitors to flowers, but they may be less important pollinators than specialist and generalist avian nectarivores. This study provides further insight into the pollination biology of a diverse, and ecologically important, succulent genus in Africa.
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    The sixth World Flora Online Council meeting held in South Africa
    (AOSIS (pty) Ltd, 2017) le Roux, M.; Klopper, R.; Jackson, P.S.W.; Loizeau, P.; Victor, J.E.; Sebola, J.R.
    Biannual Council meetings are held with the aim of developing a World Flora Online (WFO) in response to Target 1 of the Global Strategy for Plant Conservation (2011-2020). Objectives: To report on the sixth WFO Council meeting held in Pretoria, South Africa, on November 2016. Method: A WFO Council meeting (preceded by Taxonomic and Technical Working Group meetings) was hosted by the South African National Biodiversity Institute in Pretoria. Results: Significant progress with the development of the WFO portal was made. Conclusion: The WFO portal will be launched at the International Botanical Congress in China in 2017.
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    Both thyroid hormone levels and resting metabolic rate decrease in African striped mice when food availability decreases
    (Company of Biologists Ltd, 2017-03) Rimbach, R.; Pillay, N.; Schradin, C.
    In response to variation in food availability and ambient temperature (Ta), many animals show seasonal adaptations in their physiology. Laboratory studies showed that thyroid hormones are involved in the regulation of metabolism, and their regulatory function is especially important when the energy balance of an individual is compromised. However, little is known about the relationship between thyroid hormones and metabolism in free-living animals and animals inhabiting seasonal environments. Here, we studied seasonal changes in triiodothyronine (T3) levels, resting metabolic rate (RMR) and two physiological markers of energy balance (blood glucose and ketone bodies) in 61 free-living African striped mice (Rhabdomys pumilio) that live in an semi-arid environment with food shortage during the dry season. We predicted a positive relationship between T3 levels and RMR. Further, we predicted higher T3 levels, blood glucose levels and RMR, but lower ketone body concentrations, during the moist season when food availability is high compared with summer when food availability is low. RMR and T3 levels were negatively related in the moist season but not in the dry season. Both RMR and T3 levels were higher in the moist than in the dry season, and T3 levels increased with increasing food availability. In the dry season, blood glucose levels were lower but ketone body concentrations were higher, indicating a change in substrate use. Seasonal adjustments in RMR and T3 levels permit a reduction of energy expenditure when food is scarce, and reflect an adaptive response to reduced food availability in the dry season.
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    Stable isotope (δ13C) profiling of xylitol and sugar in South Africa
    (Academy of Science of South Africa (ASSAf), 2017-05) Symes, C.; Loubser, E.; Woodborne, S.
    Xylitol is an alternative sweetener to sucrose, glucose and fructose, and is available under a number of brands in South Africa. Carbon stable isotope values (δ13C) of a selection of commercially available xylitol products (n=28) were analysed and compared with sugar samples (n=29). Sugarcane (C4) and beet sugar (C3) derived sugar samples aligned with published values of source, although two samples that indicated a sugarcane origin suggested a beet sugar origin. Control corn-derived samples defined a stepwise xylose to xylitol discrimination of +0.7‰. The distinction between C3- and C4-derived xylitol was less clear with three samples difficult to define (range = -14.8 to -17.1‰). The values for a suite of xylitol samples (-22.3‰ to -19.7‰; n=8) that aligned closely with a suspected C3-derived xylose, were ~8‰ more positive than known birch isotope values. Some xylitol samples may thus represent (1) a mixture of C3- and C4-derived products, (2) derivation from a CAM species source or (3) different processing techniques in which the discrimination values of xylose from corn, and xylose from birch, may differ because of the respective chemical processing techniques. No samples that claimed a birch bark origin were within the range of samples suggested to be corn derived (i.e. -13.0‰ to -9.7‰, n=16). We suggest that the threshold values provided are relatively robust for defining the origins of xylitol and sugar, and can be used in determining the authenticity and claims of suppliers and producers.
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    Determinants of seasonal changes in availability of food patches for elephants (Loxodonta africana) in a semi-arid African savanna
    (PeerJ Inc., 2017-06) Clegg, B.W.; O'Connor, T.G.
    Loss of biodiversity caused by impact of elephants (Loxodonta africana) on African woodlands may require a management response, but any action should be based on an understanding of why elephants choose to utilise trees destructively. Comprehension of elephant feeding behaviour requires consideration of the relative value of the plant groups they may potentially consume. Profitability of available food is partly determined by the time to locate a food patch and, therefore, as a foundation for understanding the influence of food availability on diet selection, key controls on the density of grass, forb, and browse patches were investigated across space and time in a semi-arid African savanna. Density of food patches changed seasonally because plant life-forms required different volumes of soil water to produce green forage; and woody plants and forbs responded to long-term changes in soil moisture, while grasses responded to short-term moisture pulses. Soil texture, structure of woody vegetation and fire added further complexity by altering the soil water thresholds required for production of green forage. Interpolating between regularly-timed, ground-based measurements of food density by using modelled soil water as the predictor in regression equations may be a feasible method of quantifying food available to elephants in complex savanna environments.
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    Using genetics to prioritise headwater stream fish populations of the Marico barb, Enteromius motebensis Steindachner 1894, for conservation action.
    (AOSIS OpenJournals Publishing AOSIS (Pty) Ltd, 2017-02) van der Walt, K.-A.; Swartz, E.R.; Woodford, D.J.; Weyl, O.
    South Africa has a relatively large number of threatened freshwater fish species and limited resources to implement conservation programs. Enteromius motebensis was regionally prioritised for action because of its conservation status and flagship status in a nationally important aquatic ecosystem. Genetic diversity of E. motebensis in headwater refugia of the Groot Marico River Catchment was assessed to determine if genetic diversity is important for conservation planning for this species. The results of the genetic analysis indicate that some prioritisation was possible, with two populations showing evidence of recent isolation. Conservation implications: We recommend that at least three populations be prioritised for conservation action to ensure maintenance of most of the remaining genetic diversity of the species.
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    Demographics of Eucalyptus grandis and implications for invasion
    (AOSIS OpenJournals Publishing AOSIS (Pty) Ltd, 2017-03) Musengi, K.; Archibald, S.
    Alien invasive species can have negative impacts on the functioning of ecosystems. Plantation species such as pines have become serious invaders in many parts of the world, but eucalypts have not been nearly as successful invaders. This is surprising considering that in their native habitat they dominate almost all vegetation types. Available theory on the qualities that characterise invasive species was used to assess the invasive potential of Eucalyptus grandis - a common plantation species globally. To determine rates of establishment of E. grandis outside plantations, we compared population demographics and reproductive traits at two locations in Mpumalanga, South Africa: one at higher elevation with more frost. Eucalyptus grandis has a short generation time. We found no evidence that establishment of E. grandis was limiting its spread into native grassland vegetation, but it does appear that recruitment is limited by frost and fire over much of its range in Mpumalanga. Populations at both study locations this played characteristics of good recruitment. Size class distributions showed definite bottlenecks to recruitment which were more severe when exposed to frost at higher elevations. Generally, the rate of spread is low suggesting that the populations are on the establishing populations’ invasion stage. This research gives no indication that there are any factors that would prevent eucalyptus from becoming invasive in the future, and the projected increase in winter temperatures should be a cause for concern as frost is currently probably slowing recruitment of E. grandis across much of its planted range. Conservation implications: Eucalyptus plantations occur within indigenous grasslands that are of high conservation value. Frost and fire can slow recruitment where they occur, but there are no obvious factors that would prevent E. grandis from becoming invasive in the future, and monitoring of its rates of spread is recommended.
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    Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil
    (Nature Publishing Group, 2017-01) Gunnigle, E.; Frossard, A.; Guerrero, L.; Seely, M.; Cowan, D.A.; Ramond, J.-B.
    Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were 'time-of-day-dependent' which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module 'hubs' orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.
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    Uptake of silicon by sugarcane from applied sources may not reflect plant-available soil silicon and total silicon content of sources
    (Frontiers Media S.A., 2017-05) Keeping, M.G.
    Soils of the tropics and sub-tropics are typically acid and depleted of soluble sources of silicon (Si) due to weathering and leaching associated with high rainfall and temperatures. Together with intensive cropping, this leads to marginal or deficient plant Si levels in Si-accumulating crops such as rice and sugarcane. Although such deficiencies can be corrected with exogenous application of Si sources, there is controversy over the effectiveness of sources in relation to their total Si content, and their capacity to raise soil and plant Si concentrations. This study tested the hypothesis that the total Si content and provision of plant-available Si from six sources directly affects subsequent plant Si uptake as reflected in leaf Si concentration. Two trials with potted cane plants were established with the following Si sources as treatments: calcium silicate slag, fused magnesium (thermo) phosphate, volcanic rock dust, magnesium silicate, and granular potassium silicate. Silicon sources were applied at rates intended to achieve equivalent elemental soil Si concentrations; controls were untreated or lime-treated. Analyses were conducted to determine soil and leaf elemental concentrations. Among the sources, calciumsilicate produced the highest leaf Si concentrations, yet lower plant-available soil Si concentrations than the thermophosphate. The latter, with slightly higher total Si than the slag, produced substantially greater increases in soil Si than all other products, yet did not significantly raise leaf Si above the controls. All other sources did not significantly increase soil or leaf Si concentrations, despite their high Si content. Hence, the total Si content of sources does not necessarily concur with a product’s provision of soluble soil Si and subsequent plant uptake. Furthermore, even where soil pH was raised, plant uptake from thermophosphate was well below expectation, possibly due to its limited liming capacity. The ability of the calcium silicate to provide Si while simultaneously and significantly increasing soil pH, and thereby reducing reaction of Si with exchangeable Al3+, is proposed as a potential explanation for the greater Si uptake into the shoot from this source.