Short‐term harvesting of biomass from conservation grasslands maintains plant diversity

High yields are a priority in managing biomass for renewable energy, but the environmental impacts of various feedstocks and production systems should be equally considered. Mixed‐species, perennial grasslands enrolled in conservation programs are being considered as a source of biomass for renewable energy. Conservation grasslands are crucial in sustaining native biodiversity throughout the US Upper Midwest, and the effects of biomass harvest on biodiversity are largely unknown. We measured the effect of late‐season biomass harvest on plant community composition in conservation grasslands in three regions of Minnesota, USA from 2009 to 2012. Temporal trends in plant species composition within harvested grasslands were compared to unharvested grasslands using mixed effects models. A before‐after control‐impact approach using effect sizes was applied to focus on pre‐ and postharvest conditions. Production‐scale biomass harvest did not affect plant species richness, species or functional group diversity, nor change the relative abundance of the main plant functional groups. Differences in the relative abundances of plant functional groups were observed across locations; and at some locations, changed through time. The proportion of non‐native species remained constant, while the proportion of noxious weeds decreased through time in both harvested and unharvested grasslands at the central location. Ordination revealed patterns in species composition due to location, but not due to harvest treatment. Therefore, habitat and bioenergy characteristics related to grassland plant communities are not expected to change due to short‐term or intermittent late‐season biomass harvest.     

The importance of food supply in high‐productivity ecosystems: Short‐term experimental tests with small rodents

Food availability is considered to be a primary factor affecting animal populations, yet few experimental tests have been performed to evaluate its actual importance in species‐rich ecosystems such as rainforests. It has been suggested that in such systems certain plant species may act as “keystone” resources for animals, but the importance of presumed keystone resources for populations has not been quantified experimentally. Using complementary seed removal and seed‐addition experiments, we determined how the supply of a presumed keystone resource, seeds of Araucaria angustifolia, affects short‐term demography of their main consumer group (small rodents) in a biodiversity hotspot, the Brazilian Atlantic Forest. We hypothesized that (i) the harvest of A. angustifolia seeds by human populations has negative impacts on rodents, and (ii) these seeds are a limiting resource for rodent populations. To test these hypotheses, we monitored populations of two species of numerically dominant rodents (Delomys dorsalis and Akodon montensis) within replicated control‐experimental plots. Manipulations of seed supply over 2 years had little effect on population size, body condition, survival, or reproduction of the two rodents, suggesting that, in the short‐term (within one generation), their populations are not food limited in Araucaria forests. Despite apparently having all the characteristics of a keystone resource, as currently defined in the literature, the seeds of A. angustifolia had limited influence on the short‐term demography of their main consumer group. In situations where purported keystone resources are seasonally abundant, their actual importance may be lower than generally assumed, and these resources then may have only localized and temporary effects on consumer populations.     

Long‐term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA

Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high‐throughput sequencing to generate time‐series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high‐magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.     

Unraveling the genomic diversity of small eukaryotes

A report of the meeting Comparative Genomics of Eukaryotic Microorganisms, 17-22 October 2009, San Feliu de Guixols, Spain.     

Short‐term lime pretreatment of poplar wood

Short‐term lime pretreatment uses lime and high‐pressure oxygen to significantly increase the digestibility of poplar wood. When the treated poplar wood was enzymatically hydrolyzed, glucan and xylan were converted to glucose and xylose, respectively. To calculate product yields from raw biomass, these sugars were expressed as equivalent glucan and xylan. To recommend pretreatment conditions, the single criterion was the maximum overall glucan and xylan yields using a cellulase loading of 15 FPU/g glucan in raw biomass. On this basis, the recommended conditions for short‐term lime pretreatment of poplar wood follow: (1) 2 h, 140°C, 21.7 bar absolute and (2) 2 h, 160°C, and 14.8 bar absolute. In these two cases, the reactivity was nearly identical, thus the selected condition depends on the economic trade off between pressure and temperature. Considering glucose and xylose and their oligomers produced during 72 h of enzymatic hydrolysis, the overall yields attained under these recommended conditions follow: (1) 95.5 g glucan/100 g of glucan in raw biomass and 73.1 g xylan/100 g xylan in raw biomass and (2) 94.2 g glucan/100 g glucan in raw biomass and 73.2 g xylan/100 g xylan in raw biomass. The yields improved by increasing the enzyme loading. An optimal enzyme cocktail was identified as 67% cellulase, 12% β‐glucosidase, and 24% xylanase (mass of protein basis) with cellulase activity of 15 FPU/g glucan in raw biomass and total enzyme loading of 51 mg protein/g glucan in raw biomass. Ball milling the lime‐treated poplar wood allowed for 100% conversion of glucan in 120 h with a cellulase loading of only 10 FPU/g glucan in raw biomass. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Unraveling the genomic diversity of small eukaryotes

A report of the meeting Comparative Genomics of Eukaryotic Microorganisms, 17-22 October 2009, San Feliu de Guixols, Spain.     

Short‐term effects of a severe drought on avian diversity and abundance in a Pampas Agroecosystem

Agroecosystems are naturally variable at different scales showing strong environmental variations through time and in space. Therefore, temporal dynamics should be taken into account to understand the species‐habitat relationship and provide information for biodiversity management. Droughts are climatic events that introduce variations in environmental conditions by reducing food resources and are increasing in severity and frequency due to global climate change. In 2008, a severe drought occurred in the argentine Pampas, which allowed us to test its short‐term effect on avian diversity patterns according to different land uses. Also, we could test how variations in net primary productivity affected bird populations and explore the usefulness of this ecological process as an indicator of ecosystem service supply applicable to different ecological contexts. We surveyed bird diversity in two consecutive years (2007–2008) in the Rolling Pampas of Argentina, and we assessed environmental attributes at two spatial scales. We explored the relationship between bird diversity and an ecosystem services provision index (ESPI) that uses a proxy of net primary productivity and its intra‐annual variation to test its adequacy in the changing conditions, we conducted our surveys. Results showed that drought affected negatively both species richness and abundance as a consequence of net primary productivity reductions. There was not a clear association of diversity changes with land use, and it is probable that the effect of drought is a complex combination of productivity, land use and spatial scale. ESPI proved robust in front of the environmental changes, and its predictive capacity was better at larger scales. These results are promising for the assessment of ecosystem services provision in a context of global climate changes. Abstract in Spanish is available with online material.     

Short‐term insurance versus long‐term bet‐hedging strategies as adaptations to variable environments

Understanding how organisms adapt to environmental variation is a key challenge of biology. Central to this are bet‐hedging strategies that maximize geometric mean fitness across generations, either by being conservative or diversifying phenotypes. Theoretical models have identified environmental variation across generations with multiplicative fitness effects as driving the evolution of bet‐hedging. However, behavioral ecology has revealed adaptive responses to additive fitness effects of environmental variation within lifetimes, either through insurance or risk‐sensitive strategies. Here, we explore whether the effects of adaptive insurance interact with the evolution of bet‐hedging by varying the position and skew of both arithmetic and geometric mean fitness functions. We find that insurance causes the optimal phenotype to shift from the peak to down the less steeply decreasing side of the fitness function, and that conservative bet‐hedging produces an additional shift on top of this, which decreases as adaptive phenotypic variation from diversifying bet‐hedging increases. When diversifying bet‐hedging is not an option, environmental canalization to reduce phenotypic variation is almost always favored, except where the tails of the fitness function are steeply convex and produce a novel risk‐sensitive increase in phenotypic variance akin to diversifying bet‐hedging. Importantly, using skewed fitness functions, we provide the first model that explicitly addresses how conservative and diversifying bet‐hedging strategies might coexist.     

Quantifying long‐term recurrence in planktonic microbial eukaryotes

How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long‐term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV‐III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long‐term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non‐recurrent changes characterize the dynamics of microbial assemblages.     

Short‐term proteomic dynamics reveal metabolic factory for active extrafloral nectar secretion by Acacia cornigera ant‐plants

Despite the ecological and evolutionary importance of nectar, mechanisms controlling its synthesis and secretion remain largely unknown. It is widely believed that nectar is ‘secreted phloem sap’, but current research reveals a biochemical complexity that is unlikely to stem directly from the phloem. We used the short daily peak in production of extrafloral nectar by Acacia cornigera to investigate metabolic and proteomic dynamics before, during and after 2 h of diurnal secretion. Neither hexoses nor dominating nectar proteins (nectarins) were detected in the phloem before or during nectar secretion, excluding the phloem as the direct source of major nectar components. Enzymes involved in the anabolism of sugars, amino acids, proteins, and nectarins, such as invertase, β–1,3–glucanase and thaumatin‐like protein, accumulated in the nectary directly before secretion and diminished quantitatively after the daily secretion process. The corresponding genes were expressed almost exclusively in nectaries. By contrast, protein catabolic enzymes were mainly present and active after the secretion peak, and may function in termination of the secretion process. Thus the metabolic machinery for extrafloral nectar production is synthesized and active during secretion and degraded thereafter. Knowing the key enzymes involved and the spatio‐temporal patterns in their expression will allow elucidation of mechanisms by which plants control nectar quality and quantity.     

Fragmentation alters beta‐diversity patterns of habitat specialists within forest metacommunities

The relative importance of local, regional and historical factors in controlling the spatial patterns of plant species distribution is still poorly known and challenging for conservation ecology. We conducted an empirical study to link the spatial variation of species and environments among forest patches embedded in contrasted agricultural matrices. We compared how forest herb communities responded to spatial environmental gradients and past forest cover. We found low values of β‐diversity in both unfragmented and highly fragmented systems, independently from local and regional diversities. As fragmentation increased, the spatial structure of local plant communities was more complex and spatial effects explained an increasing proportion of β‐diversity, suggesting that the importance of dispersal limitations increased and played out at broad spatial scales. However, where spatio‐temporal isolation of forest patches was the highest, local species assemblages could not be explained, suggesting that the metacommunity functioning was disrupted. Where the historical continuity was high, local environmental characteristics explained a significant amount of species assemblages within metacommunities, suggesting habitat‐selection processes. Beta‐diversity and variations in presence–absence of species were also influenced by the intensity of landscape management, via the permeability of both forest edges and the matrix. This spatially‐explicit analysis of metacommunities revealed that forest fragmentation impacts beta‐diversity by altering not only the relative importance of deterministic and stochastic processes, but also the spatial scales at which they act. These results provide empirical support for the conservation of ancient forests and the maintenance of a high connectedness between fragments within agricultural landscapes.     

Short‐term dynamics of nest occupancy in an allopaternal species,the tessellated darter Etheostoma olmstedi

To inquire how male size interacts with alloparental behaviour and mating success in the tessellated darter Etheostoma olmstedi, males were given a choice of nests with or without eggs; subsequent nest occupancy, takeovers and egg deposits were monitored. Subordinate males readily occupied available nests with eggs but were often evicted by dominant males, suggesting that males of all sizes compete for the opportunity to provide allopaternal care in this species.     

Short‐term response of threatened small macropods and their predators to prescribed burns in subtropical Australia

Fire is an important ecological process that shapes vegetation structure and habitat for faunal assemblages globally. Prescribed burns are increasingly being used in conservation and management to restore fire regimes in fire‐suppressed vegetation communities. Small threatened macropods require structurally complex habitat that allows them to evade detection by predators. Given that fire can alter vegetation structure, it can be viewed as a strong ecological force in shifting the dynamics between predator and prey species. Previous studies in temperate Australia have shown that prescribed burns in the presence of European Red Fox (Vulpes vulpes) and feral Cat (Felis catus) can have negative impacts on small macropods and medium‐sized mammals. Post‐fire response of threatened small macropods and their predators has not been experimentally examined in subtropical Australia despite this region providing refugia for the Long‐nosed Potoroo (Potorous tridactylus) and Red‐legged Pademelon (Thylogale stigmatica). We conducted a before‐after‐control‐impact fire experiment at two paired sites after low–moderate intensity burns typical of cool season prescribed burns. We used camera trapping to investigate changes in activity of threatened small macropods and their predators. We also recorded vegetation change. Despite large reductions in ground and shrub cover, activity of small macropods and the Dingo (Canis dingo) did not change in response to fires. Therefore, the threat of dingo predation appears to have remained unchanged following the fires. Although feral cats and foxes were present, they showed negligible activity across our sites. Our study suggests that small‐scale patchy ecological burns may not lead to increased predation of small macropods in our landscape. We attribute this to sufficient post‐fire refugia and very low densities of foxes.     

Short‐ and long‐term costs of reproduction in a migratory songbird

Costs of reproduction represent a common life‐history trade‐off. Critical to understanding these costs in migratory species is the ability to track individuals across successive stages of the annual cycle. We assessed the effects of total number of offspring fledged and date of breeding completion on pre‐migratory body condition, the schedule of moult and annual survival in a migratory songbird, the Savannah Sparrow Passerculus sandwichensis. Between 2008 and 2010, moult was delayed for individuals that finished breeding later in the breeding period and resulted in reduced lean tissue mass during the pre‐migratory period, suggesting an indirect trade‐off between the timing of breeding completion and condition just prior to migration. Lean tissue mass decreased as the number of offspring fledged increased in 2009, a particularly cool and wet year, illustrating a direct trade‐off between reproductive effort and condition just prior to migration in years when weather is poor. However, using a 17‐year dataset from the same population, we found that parents that fledged young late in the breeding period had the highest survival and that number of offspring fledged did not affect survival, suggesting that individuals do not experience long‐term trade‐offs between reproduction and survival. Taken together, our results suggest that adult Savannah Sparrows pay short‐term costs of reproduction, but that longer‐term costs are mitigated by individual quality, perhaps through individual variation in resource acquisition.     

Mock communities highlight the diversity of host‐associated eukaryotes

Host‐associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High‐throughput sequencing (HTS) tools have illuminated the vast diversity of host‐associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall‐Ngai et al. 2013 ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. 2011 ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host‐associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host‐associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. 2014 ; Simon et al. 2015 ; de Vargas et al. 2015 ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. 2014 )]. In this issue of Molecular Ecology, Geisen et al. ( 2015 ) use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free‐living. By isolating the host‐associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high‐throughput sequencing (HTS) and reinforce the ubiquity of these host‐associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free‐living, but instead need to design studies that specifically enumerate the diversity and function of host‐associated eukaryotes. Doing so will allow the field to determine the role host‐associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host‐associated communities, disease ecology and more.     

Short‐term and long‐term effects of acute kidney injury in chronic kidney disease patients: A longitudinal analysis

We use data from an ongoing cohort study of chronic kidney patients at Salford Royal NHS Foundation Trust, Greater Manchester, United Kingdom, to investigate the influence of acute kidney injury (AKI) on the subsequent rate of change of kidney function amongst patients already diagnosed with chronic kidney disease (CKD). We use a linear mixed effects modelling framework to enable estimation of both acute and chronic effects of AKI events on kidney function. We model the fixed effects by a piece‐wise linear function with three change‐points to capture the acute changes in kidney function that characterise an AKI event, and the random effects by the sum of three components: a random intercept, a stationary stochastic process with Matérn correlation structure, and measurement error. We consider both multivariate Normal and multivariate t versions of the random effects. For either specification, we estimate model parameters by maximum likelihood and evaluate the plug‐in predictive distributions of the random effects given the data. We find that following an AKI event the average long‐term rate of decline in kidney function is almost doubled, regardless of the severity of the event. We also identify and present examples of individual patients whose kidney function trajectories diverge substantially from the population‐average.     

Short‐term soil carbon sink potential of oil palm plantations

Oil palm plantations cover ≈14.6 million ha worldwide and the total area under cultivation is expected to increase during the 21st century . Indonesia and Malaysia together account for 87% of global palm oil production and the combined harvested area in these countries has expanded by 6.5 million ha since 1990. Despite this, soil C cycling in oil palm systems is not well quantified but such information is needed for C budget inventories. We quantified soil C storage (root biomass, soil organic matter (SOM) and microbial biomass) and losses [potential soil respiration (R_s) and soil surface CO₂ flux (F_s)] in mineral soils from an oil palm plantation chronosequence (11–34 years since planting) in Selangor, Malaysia. There were no significant effects of plantation age on SOM, microbial biomass, R_s or F_s, implying soil C was in dynamic equilibrium over the chronosequence. However, there was a significant increase in root biomass with plantation age, indicating a short‐term C sink. Across the chronosequence, R_s was driven by soil moisture, soil particle size, root biomass and soil microbial biomass N but not microbial biomass C. This suggests that the nutrient status of the microbial community may be of equal or greater importance for soil CO₂ losses than substrate availability and also raises particular concerns regarding the addition of nitrogenous fertilizer, i.e. increased yields will be associated with increased soil CO₂ emissions. To fully assess the impact of oil palm plantations on soil C storage, initial soil C losses following land conversion (e.g. from native forest or other previous plantations) must be accounted for. If initial soil C losses are large, our data show that there is no accumulation of stable C in the soil as the plantation matures and hence the conversion to oil palm would probably represent a net loss of soil C.