Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming‐induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15–65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β‐diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic‐related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co‐evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw‐related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.     

The effect of habitat fragmentation on the bee visitor assemblages of three Australian tropical rainforest tree species

Tropical forest loss and fragmentation can change bee community dynamics and potentially interrupt plant–pollinator relationships. While bee community responses to forest fragmentation have been investigated in a number of tropical regions, no studies have focused on this topic in Australia. In this study, we examine taxonomic and functional diversity of bees visiting flowers of three tree species across small and large rainforest fragments in Australian tropical landscapes. We found lower taxonomic diversity of bees visiting flowers of trees in small rainforest fragments compared with large forest fragments and show that bee species in small fragments were subsets of species in larger fragments. Bees visiting trees in small fragments also had higher mean body sizes than those in larger fragments, suggesting that small‐sized bees may be less likely to persist in small fragments. Lastly, we found reductions in the abundance of eusocial stingless bees visiting flowers in small fragments compared to large fragments. These results suggest that pollinator visits to native trees living in small tropical forest remnants may be reduced, which may in turn impact on a range of processes, potentially including forest regeneration and diversity maintenance in small forest remnants in Australian tropical countryside landscapes.     

Effects of Potassium Chloride‐Induced Stress on the Carotenoids Canthaxanthin,Astaxanthin, and Lipid Accumulations in the Green Chlorococcal Microalga Strain TISTR 9500

Microalgae are a diverse group of photosynthetic eukaryotic organisms that are widely distributed globally. They are prolific sources of highly valuable compounds with fascinating chemical structures. Due to their balanced nutritional compositions and health benefits, they are increasingly being used as functional food ingredients. Carotenoid‐based pigments and polyunsaturated fatty acids (PUFAs) are examples of high‐value nutrients that can be accumulated abundantly in microalgae. Here, the effects of potassium chloride‐induced stress on the productions of lipids and carotenoids in the green microalga of the Chlorococcaceae family were investigated. Under normal BG11 medium, this green microalga strain TISTR 9500 accumulated high levels of PUFA and primary carotenoid lutein. Stress tests revealed that KCl enhanced and modulated lipid and carotenoid accumulation levels. The liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) analysis revealed that secondary carotenoids astaxanthin and canthaxanthin were robustly produced under KCl stress with the similar content of lutein. Further, this stress led to a significant increase in the total FA amount with the higher proportion of unsaturated FA than saturated FA. Thus, this green microalga could be an attractive and alternative natural biosource for canthaxanthin and astaxanthin, as well as for functional lipids.     

Functionally Similar Species Confer Greater Resistance to Invasion: Implications for Grassland Restoration

Plant community functional composition can be manipulated in restored ecosystems to reduce the establishment potential of invading species. This study was designed to compare invasion resistance among communities with species functionally similar or dissimilar to yellow starthistle (Centaurea solstitialis), a late‐season annual. A field experiment was conducted in the Central Valley of California with six experimental plant communities that included (1) six early‐season native annual forbs (AF); (2) five late‐season native perennials and one summer annual forb (NP); (3) a combination of three early‐season native annual forbs and three late‐season native perennials (FP); (4) six early‐season non‐native annual grasses (AG); (5) monoculture of the late‐season native perennial grass Elymus glaucus (EG); and (6) monoculture of the late‐season native perennial Grindelia camporum (GC). Following establishment, C. solstitialis seed was added to half of the plots, and a monoculture of C. solstitialis (CS) was established as a control. Over a 5‐year period, the AF and AG communities were ineffective at preventing C. solstitialis invasion. Centaurea solstitialis cover remained less than 10% in the FP and NP communities, except in year 1. By the fourth year, E. glaucus cover was greater than 50% in NP and FP communities and had spread to all other communities (e.g., 27% cover in CS in year 5). Communities containing E. glaucus, which is functionally similar to C. solstitialis, better resisted invasion than communities lacking a functional analog. In contrast, G. camporum, which is also functionally similar to C. solstitialis, failed to survive. Consequently, species selection for restored communities must consider not only functional similarity to the invader but also establishment success, competitiveness, and survivorship.     

Comparing microscopic counts and pigment analyses in 46 phytoplankton communities from lakes of different trophic state

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Functional identity is the main driver of diversity effects in young tree communities

Two main effects are proposed to explain biodiversity–ecosystem functioning relationships: niche complementarity and selection effects. Both can be functionally defined using the functional diversity (FD) and functional identity (FI) of the community respectively. Herein, we present results from the first tree diversity experiment that separated the effect of selection from that of complementarity by varying community composition in high‐density plots along a gradient of FD, independent of species richness and testing for the effects of FD and community weighted means of traits (a proxy for FI) on stem biomass increment (a proxy for productivity). After 4 years of growth, most mixtures did not differ in productivity from the averages of their respective monocultures, but some did overyield significantly. Those positive diversity effects resulted mostly from selection effects, primarily driven by fast‐growing deciduous species and associated traits. Net diversity effect did not increase with time over 4 years.     

Geographic mosaic of symbiont selectivity in a genus of epiphytic cyanolichens

In symbiotic systems, patterns of symbiont diversity and selectivity are crucial for the understanding of fundamental ecological processes such as dispersal and establishment. The lichen genus Nephroma (Peltigerales, Ascomycota) has a nearly cosmopolitan distribution and is thus an attractive model for the study of symbiotic interactions over a wide range of spatial scales. In this study, we analyze the genetic diversity of Nephroma mycobionts and their associated Nostoc photobionts within a global framework. The study is based on Internal Transcribed Spacer (ITS) sequences of fungal symbionts and tRNA^Leu (UAA) intron sequences of cyanobacterial symbionts. The full data set includes 271 Nephroma and 358 Nostoc sequences, with over 150 sequence pairs known to originate from the same lichen thalli. Our results show that all bipartite Nephroma species associate with one group of Nostoc different from Nostoc typically found in tripartite Nephroma species. This conserved association appears to have been inherited from the common ancestor of all extant species. While specific associations between some symbiont genotypes can be observed over vast distances, both symbionts tend to show genetic differentiation over wide geographic scales. Most bipartite Nephroma species share their Nostoc symbionts with one or more other fungal taxa, and no fungal species associates solely with a single Nostoc genotype, supporting the concept of functional lichen guilds. Symbiont selectivity patterns within these lichens are best described as a geographic mosaic, with higher selectivity locally than globally. This may reflect specific habitat preferences of particular symbiont combinations, but also the influence of founder effects.     

Genomewide landscape of gene–metabolome associations in Escherichia coli

Metabolism is one of the best‐understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non‐enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single‐celled organisms. Here, we systematically mapped the association between > 3,800 single‐gene deletions in the bacterium Escherichia coli and relative concentrations of > 7,000 intracellular metabolite ions. Beyond expected metabolic changes in the proximity to abolished enzyme activities, the association map reveals a largely unknown landscape of gene–metabolite interactions that are not represented in metabolic models. Therefore, the map provides a unique resource for assessing the genetic basis of metabolic changes and conversely hypothesizing metabolic consequences of genetic alterations. We illustrate this by predicting metabolism‐related functions of 72 so far not annotated genes and by identifying key genes mediating the cellular response to environmental perturbations.     

Functional anatomy of the cervical region in the late Miocene amphicyonid Magericyon anceps (Carnivora,Amphicyonidae): implications for its feeding behaviour

We describe the skull and neck morphology of the late Miocene amphicyonid Magericyon anceps, focusing on aspects related to functional anatomy. This species, recorded only from the Vallesian sites of Batallones‐1 and Batallones‐3 (Madrid, Spain), is the last known amphicyonid in the fossil record of Western Europe, with the Batallones populations being one of the best‐known of the family. The morphology of its skull and cervical vertebrae allows us to infer aspects of its associated musculature, such as muscle strength and range of movement. Magericyon anceps had well‐developed neck muscles, suited for providing the head with a high capacity for lateral and rotatory movements, as well as for playing an important role in the extension and stabilization of the head and neck, improving its efficiency in killing and consuming prey. Magericyon anceps shared its habitat with other large carnivorans, which would have strongly influenced its behaviour. Rapid killing and processing of prey would have been an advantage for avoiding kleptoparasitism by other large predators, as well as reducing consumption time, during which M. anceps would have been more vulnerable to attack from competitors.     

High local trait variability in a globally invasive cyanobacterium

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Hydrodynamic advantages in the free‐living spiriferinide brachiopod Pachycyrtella omanensis: functional insight into adaptation to high‐energy flow environments

Immobile benthic organisms lacking attachment or cementation mechanisms are considered to be best adapted to quiet bottom environments. Since the free‐living Lower Permian spiriferinide brachiopod Pachycyrtella omanensis inhabited a sandy substrate with high‐energy water flow, flume experiments were performed to show the possible hydrodynamic advantages of shell morphology in postural stability and generation of feeding flows. Modelling indicates that a vertical position, with the commissure plane perpendicular to the seabed, was the most unstable, although it is considered to have been its original life position. On the other hand, the passive flow inside the model in vertical position exhibited vortex movement with constant degree of inhalent flow and exhalent flow, conferring advantages on the effective filtration of food particles using a spiral lophophore. The intensity and movement of the passive flow for feeding could have been adjusted through changes in the angle of opening of the valves. As the shoreface habitat was affected by oscillatory flows, a small‐sized animal could have undergone a high risk of burial, while an increase in size would have led to easier removal from the sandy bottom. To avoid both physical risks, Pachycyrtella developed a thick shell with a high rate of growth, specifically increasing the weight of the ventral umbo without altering its morphofunction to generate passive feeding flows. Biomechanics, functional morphology, opportunistic species, Pachycyrtella, Spiriferinida, suspension feeder.     

Do understorey or overstorey traits drive tree encroachment on a drained raised bog?

• One of the most important threats to peatland ecosystems is drainage, resulting in encroachment of woody species. Our main aim was to check which features – overstorey or understorey vegetation – are more important for shaping the seedling bank of pioneer trees colonising peatlands (Pinus sylvestris and Betula pubescens). We hypothesised that tree stand parameters will be more important predictors of natural regeneration density than understorey vegetation parameters, and the former will be negatively correlated with species diversity and richness and also with functional richness and functional dispersion, which indicate a high level of habitat filtering.
• The study was conducted in the ‘Zielone Bagna’ nature reserve (NW Poland). We assessed the structure of tree stands and natural regeneration (of B. pubescens and P. sylvestris) and vegetation species composition. Random forest and DCA were applied to assess relationships between variables studied.
• Understorey vegetation traits affected tree seedling density (up to 0.5‐m height) more than tree stand traits. Density of older seedlings depended more on tree stand traits. We did not find statistically significant relationships between natural regeneration densities and functional diversity components, except for functional richness, which was positively correlated with density of the youngest tree seedlings.
• Seedling densities were higher in plots with lower functional dispersion and functional divergence, which indicated that habitat filtering is more important than competition. Presence of an abundant seedling bank is crucial for the process of woody species encroachment on drained peatlands, thus its dynamics should be monitored in protected areas.

     

Host identity and phylogeny shape the foliar endophytic fungal assemblages of Ficus

Foliar endophytic fungi (FEF) are diverse and ubiquitously associated with photosynthetic land plants. However, processes shaping FEF assemblages remain poorly understood. Previous studies have indicated that host identity and host habitat are contributing factors, but these factors are often difficult to disentangle. In this study, we studied FEF assemblages from plants grown in a botanical garden, enabling us to minimize the variation in abiotic environmental conditions and fungal dispersal capacity. FEF assemblages from 46 Ficus species were sequenced using next‐generation methods, and the results indicated that closely related host species had clearly differentiated FEF assemblages. Furthermore, host phylogenetic proximity was significantly correlated with the similarity of their FEF assemblages. In the canonical correspondence analysis, eleven leaf traits explained 32.9% of the total variation in FEF assemblages, whereas six traits (specific leaf area, leaf N content, leaf pH, toughness, latex alkaloid content, and latex volume per leaf area) were significant in the first two dimensions of ordination space. In the multiple regression on distance matrix analysis, 21.0% of the total variance in FEF assemblage was explained by both host phylogeny and leaf traits while phylogeny alone explained 7.9% of the variance. Thus, our findings suggest that both evolutionary and ecological processes are involved in shaping FEF assemblages.     

Functional genotypes are associated with commensal Escherichia coli strain abundance within‐host individuals and populations

The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales is linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of commensal Escherichia coli strains were associated with within‐host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.     

Limited influence of local and landscape factors on finescale gene flow in two pond‐breeding amphibians

Dispersal and gene flow within animal populations are influenced by the composition and configuration of the landscape. In this study, we evaluated hypotheses about the impact of natural and anthropogenic factors on genetic differentiation in two amphibian species, the spotted salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus) in a commercial forest in central Maine. We conducted this analysis at two scales: a local level, focused on factors measured at each breeding pond, and a landscape level, focused on factors measured between ponds. We investigated the effects of a number of environmental factors in six categories including Productivity, Physical, Land Composition, Land Configuration, Isolation and Location. Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood frog breeding ponds. We used a hierarchical Bayesian approach in the program GESTE at each breeding pond and a random forest algorithm in conjunction with a network analysis between the ponds. We found overall high genetic connectivity across distances up to 17 km for both species and a limited effect of natural and anthropogenic factors on gene flow. We found the null models best explained patterns of genetic differentiation at a local level and found several factors at the landscape level that weakly influenced gene flow. This research indicates multiscale investigations that incorporate local and landscape factors are valuable for understanding patterns of gene flow. Our findings suggest that dispersal rates in this system are high enough to minimize genetic structuring and that current forestry practices do not significantly impede dispersal.     

Survival of a specialist natural enemy experiencing resource competition with an omnivorous predator when sharing the invasive prey Tuta absoluta

Can specialist natural enemies persist in ecosystems when competing with omnivorous natural enemies for their shared prey? The consequences of omnivory have been studied theoretically, but empirical studies are still lacking. Omnivory is nevertheless common in nature and omnivorous predators coexist with specialists in many ecosystems, even when they are intraguild predators. This type of association is also common in agroecosystems in which biological control strategies are used. Our study provides an example of the outcome of such an association in the context of biological control of the invasive pest Tuta absoluta (Lepidoptera) in a tomato agroecosystem. The two natural enemies involved, that is, a specialist (Stenomesius japonicus (Hymenoptera) parasitoid) and an omnivore (Macrolophus pygmaeus (Hemiptera) predator), were able to coexist for 3 months in our experimental cages in the absence of metacommunity mechanisms (i.e., emigration and recolonization), contrary to theoretical expectations. However, they negatively affected each other's population dynamics. We found that spatial resource segregation was not a mechanism that promoted their coexistence. Regarding pest control, the specialist and omnivorous natural enemies were found to exhibit complementary functional traits, leading to the best control when together. Mechanisms that may have promoted the coexistence of the two species as well as consequences with regard to the inoculative biological control program are discussed.