Evidence for longitudinal migration by a “sedentary” Brazilian flycatcher,the Ash‐throated Casiornis

The digitalization of museum collections and concurrent increase in citizen‐science initiatives is ushering in an era of unprecedented availability of primary biodiversity data. These changes permit a reappraisal of phenological patterns of tropical species. I examined spatio‐temporal variation in the distribution patterns of an ostensibly sedentary endemic Brazilian flycatcher, the Ash‐throated Casiornis (Casiornis fuscus), using both specimen data from museums and sighting records and rich media data from citizen‐science initiatives. I found compelling evidence for partial intratropical longitudinal migration to Amazonia and the Cerrado biomes from the species’ core range in the semi‐desert Caatinga biome and adjacent ecotones. These records from outside of the Caatinga were distributed during the height of the dry season from April to October, although the Caatinga is not entirely vacated at this time. This pattern of partial migration leads to a doubling of the distributional range of Ash‐throated Casiornises and strongly suggests that the species is a breeding near‐endemic of the Caatinga biome. This pattern was potentially previously not apparent because of significant biases in specimen collection between biomes, giving a false sense of abundance in the Brazilian Amazon.     

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses

Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture‐independent and ‐dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free‐range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.     

Aedes (Stegomyia) aegypti and Aedes (Howardina) cozumelensis in Yucatán State,México,with a summary of published collection records for Ae. cozumelensis

We collected mosquito immatures from artificial containers during 2010–2011 from 26 communities, ranging in size from small rural communities to large urban centers, located in different parts of Yucatán State in southeastern México. The arbovirus vector Aedes (Stegomyia) aegypti was collected from all 26 examined communities, and nine of the communities also yielded another container‐inhabiting Aedes mosquito: Aedes (Howardina) cozumelensis. The communities from which Ae. cozumelensis were collected were all small rural communities (<6,000 inhabitants) in the north‐central part of Yucatán State. These new collection records for Ae. cozumelensis demonstrate that this mosquito has a far broader geographic range in the Yucatán Peninsula than previously known. Ae. cozumelensis immatures were collected from both residential premises and cemeteries, with specimens recovered from rock holes as well as various artificial containers including metal cans, flower vases, buckets, tires, and a water storage tank. The co‐occurrence with Ae. aegypti in small rural communities poses intriguing questions regarding linkages between these mosquitoes, including the potential for direct competition for larval development sites. Additional studies are needed to determine how commonly Ae. cozumelensis feeds on human blood and whether it is naturally infected with arboviruses or other pathogens of medical or veterinary importance. We also summarize the published records for Ae. cozumelensis, which are restricted to collections from México's Yucatán Peninsula and Belize, and uniformly represent geographic locations where Ae. aegypti can be expected to occur.     

Capsule Treatments to Enhance Seedling Emergence of Gaura neomexicana ssp. coloradensis

Management of riparian vegetation is difficult because these communities are frequently impacted by herbivores, invasive weeds, and altered hydrologic regimes. Multiple and intertwined factors affecting rare species recruitment are particularly difficult to identify. Gaura neomexicana ssp. coloradensis Munz (Gaura) is a short‐lived perennial forb endemic to riparian areas in mixed‐grass prairies of Wyoming, Nebraska, and Colorado, U.S.A. It became a federally listed threatened species in October 2000. Because the species is a recruitment‐limited monocarpic perennial, we studied the effects of six capsule‐collection dates, a 2‐month cool‐moist stratification, 24‐hr leaching, and 24‐hr imbibition on Gaura seedling emergence. Seedling emergence did not vary with collection date. Capsules collected from Gaura plants grown at the Bridger Plant Materials Center in Montana exhibited greater emergence than capsules harvested from endemic populations near Cheyenne, Wyoming, suggesting that maternal plant growing conditions impact dormancy. Because cool‐moist stratification enhanced seedling emergence of Gaura and leaching did not, sufficient moisture during cool temperatures may be more critical than leaching of germination inhibitors as might occur with normal stream flows. Spring flooding may enhance Gaura recruitment by increasing the availability of riparian sites that are inundated during periods of cool temperatures. If so, hydrologic and climatic regimes must be considered in restoring the unique conditions needed for germination of this rare riparian endemic.     

Art/Artefact/Commodity: Installation design and the exhibition of Oceanic things at two New York museums in the 1940s

This article documents some of the experimentation in museum installation designs for the exhibition of non‐Western objects during the 1930s and 1940s. This is a period in which ethnographic artefacts were being displayed as artworks in natural history museums and in which the exhibition of such objects in art museums drew on techniques characteristic of not only natural history museums, but also commercial urban window displays (which were themselves enjoying a period of dazzling exuberance). The article focuses on one collection of Pacific Islands objects now housed at the Buffalo Museum of Science and on the installation designs of René d’Harnoncourt and Trevor Thomas. It responds to the provocation of Alfred Gell’s influential writings on art and agency, specifically, his conception of art as entrapment and enchantment—his claim that artworks captivate, and thus exert a kind of (secondary) agency on people (patients).     

Clumping behavior and byssus production as strategies for substrate competition in Mytilus edulis

Laboratory experiments showed that the mussel Mytilus edulis aggregated more intensely around living organisms (the bivalve Hiatella arctica and the solitary ascidian Styela rustica, which commonly co‐occur with mussels in fouling communities) than around inanimate objects. When exposed to an inanimate object, mussels attached their byssal threads primarily to the substrate, close to the object, but when exposed to a living organism, they attached their byssal threads directly to the organism. The ascidian was more intensely covered with byssal threads than was the bivalve. Mussel attachment to the ascidians was apparently determined by the physical characteristics of the tunic and to a lesser extent by the excretion‐secretion products released by S. rustica. This study indicates that mussels can use byssus threads as a means of entrapment of potential competitors for space. It remains unclear why mussels preferentially attached to ascidians compared to the bivalve. This can be explained either by competitive interactions, or by attractiveness of the ascidian tunic as an attachment substratum.     

Secondary successional trajectories of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere‐associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere‐associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long‐term succession of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar, we carried out a 2‐year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil‐spill site. Vegetated and un‐vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late‐phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early‐phase communities. The high‐dominance/low‐diversity functional gene communities underwent a transition to low‐dominance/high‐diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.     

The canopy beetle faunas of Gondwanan element trees in Chilean temperate rain forests

Aim To describe the coleopteran fauna occurring in canopies of temperate Gondwanan tree species in terms of their diversity and guild and taxonomic structures, and to test the proposition that this structuring reflects the Gondwanan origins of this fauna. Location The Andes and the coastal cordillera of temperate Chile. Methods Canopy fogging was used to sample beetles from 29 trees. The samples were statistically described using S_chao and the Simpson diversity index D. Cluster analyses and multi‐dimensional scaling (MDS) were performed. The taxonomic and guild structures of the Chilean coleopteran fauna were compared quantitatively with those found in other parts of the world using homogeneity chi‐square and t‐tests. Results A collection of 25,497 beetle specimens was obtained primarily from Nothofagus dombeyi, Nothofagus obliqua and Araucaria araucana. The specimens collected were distributed between 485 morphospecies and included 107 putative, new generic‐level taxa and 223 apparently undescribed species. Estimates of the size of the canopy beetle fauna showed that 600+ species were likely to be present. The communities found on a tree species differed markedly between years. MDS plots showed less community divergence between tree species for predators than for phytophages and xylophages. The guild structure was similar to that found on Australian ‘Gondwanan’ trees but differed significantly from the community structures found on ‘Laurasian’ tropical and temperate trees in supporting fewer phytophages and saprophages, but more xylophages. The predator guild showed a different pattern, with tropical faunas differing from those of more temperate regions, irrespective of hemisphere, as did the distribution of superfamilies. Main conclusions The beetle fauna found in the canopies of N. dombeyi, N. obliqua and A. araucana was large (600+ species), with about half of the species undescribed. S_chao was found to vary with sample size and to give lower estimates of S than species attenuation curves, raising the possibility that the two methods are estimating the sizes of different statistical communities. It is possible that the attenuation curve is estimating the number of species to be found on a particular tree species, while S_chao is estimating the ‘carrying capacity’ for beetle species of individual trees, and this varies from tree to tree. Care also needs to be taken in experimental design when monitoring temporal changes in forest insect communities given the difference in communities found between years in this study. The proportions of phytophages, saprophages and xylophages resemble those of a ‘Gondwanan’ rain forest from Australia and differ significantly from those of tropical and temperate ‘Laurasian’ forests.     

Desert spring refugia: museums of diversity or evolutionary cradles?

Refugia play a critical role in preserving species unable to move or adapt to cope with environmental change. The role of refugia as ‘museums of diversity’ means these environments have a high conservation priority. Less well known, however, is the role that isolated and fragmented refugia can play in the generation of new diversity. Here, we examined the diversification and evolutionary history of a community of endemic invertebrates that inhabit Australian desert spring refugia. We compared the phylogenies of seven endemic groups (Haloniscus and Phreatomerus isopods, chiltoniid amphipods, Ngarawa ostracods, Trochidrobia and Fonscochlea snails and Gymnochthebius beetles) from these springs and examine the rates and timing of diversification and reconstructed the phylogeographic history of each taxon. Despite major life‐history differences among these taxa, they demonstrate remarkable similarities in their evolutionary histories. All groups have multiple lineages that extend back to a time before the formation of present‐day deserts, and significant geographic‐based diversification since adapting to a refugial habitat. The results provide further evidence that refugia act as museums of biodiversity, preserving lineages that would have otherwise gone extinct. However, we also observed that isolation in refugia corresponds with significant diversification, leading to a recently evolved, novel endemic fauna, supporting the idea that fragmented refugia provide ideal conditions for the generation of future biodiversity hotspots.     

Early succession on plots with the upper soil horizon removed

Abstract. Succession was studied on plots with the upper soil horizon removed in an area affected by acidic air pollution in the Kru?né Hory Mts., Czech Republic. 10 permanent 1‐m² plots were marked and vegetation recorded annually using a grid of 100 subplots from 1989 to 1995. Constrained ordination analyses showed that soil texture is the most important environmental factor influencing the course of succession. Its effect on species composition increases with successional age of the plant community. On fine‐grained soils species‐poor communities dominated by grasses (Calamagrostis villosa, Deschampsiaflexuosa) and on coarse‐grained soils species‐rich communities dominated by heather (Calluna vulgaris) developed. Succession proceeded from communities where species composition was determined by diaspore availability towards communities where species composition depended on environmental conditions. Successional communities after 10 yr are more dependent on soil characteristics and consequently environmental determination increases over the course of succession and causes the communities to diverge.     

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands?

Invasive plants are often associated with greater productivity and soil nutrient availabilities, but whether invasive plants with dissimilar traits change decomposer communities and decomposition rates in consistent ways is little known. We compared decomposition rates and the fungal and bacterial communities associated with the litter of three problematic invaders in intermountain grasslands; cheatgrass (Bromus tectorum), spotted knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula), as well as the native bluebunch wheatgrass (Pseudoroegneria spicata). Shoot and root litter from each plant was placed in cheatgrass, spotted knapweed, and leafy spurge invasions as well as remnant native communities in a fully reciprocal design for 6 months to see whether decomposer communities were species‐specific, and whether litter decomposed fastest when placed in a community composed of its own species (referred to hereafter as home‐field advantage–HFA). Overall, litter from the two invasive forbs, spotted knapweed and leafy spurge, decomposed faster than the native and invasive grasses, regardless of the plant community of incubation. Thus, we found no evidence of HFA. T‐RFLP profiles indicated that both fungal and bacterial communities differed between roots and shoots and among plant species, and that fungal communities also differed among plant community types. Synthesis. These results show that litter from three common invaders to intermountain grasslands decomposes at different rates and cultures microbial communities that are species‐specific, widespread, and persistent through the dramatic shifts in plant communities associated with invasions.     

Amplification success rate of DNA from museum skin collections: a case study of stoats from 18 museums

There are large museum collections of mammalian skins and we wished to determine their usefulness for DNA‐based evolutionary and conservation studies. Methods derived from the ancient DNA approach were used to process samples from skins of the stoat (Mustela erminea) from 18 museums in 11 countries. Successful polymerase chain reaction (PCR) amplification was achieved in 56%, 46% and 40% of all samples for 0.65‐, 0.70‐ and 0.78‐kb PCR products of mitochondrial DNA, respectively. Some of the best‐preserved skin samples were those in tight‐fitting containers in a dry and cold environment. With care in their preservation, mammalian skin collections may be a good source of DNA.     

Taxonomic and functional diversity of atrazine‐degrading bacterial communities enriched from agrochemical factory soil

Aims: To characterize atrazine‐degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. Methods and Results: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65–80% of ¹⁴C ring‐labelled atrazine. The presence of trzN‐atzBC‐trzD, trzN‐atzABC‐trzD and trzN‐atzABCDEF‐trzD gene combinations was determined by PCR. In all enriched communities, trzN‐atzBC genes were located on a 165‐kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α‐, β‐ and γ‐subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine‐degrading community members previously isolated from the same contaminated site. Conclusions: The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine‐catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine. Significance and Impact of the Study: This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long‐term contamination by s‐triazine compounds.     

Community dynamics of nematodes after Larsen ice‐shelf collapse in the eastern Antarctic Peninsula

Free‐living marine nematode communities of the Larsen B embayment at the eastern Antarctic Peninsula were investigated to provide insights on their response and colonization rate after large‐scale ice‐shelf collapse. This study compares published data on the post‐collapse situation from 2007 with new material from 2011, focusing on two locations in the embayment that showed highly divergent communities in 2007 and that are characterized by a difference in timing of ice‐shelf breakup. Data from 2007 exposed a more diverse community at outer station B.South, dominated by the genus Microlaimus. On the contrary, station B.West in the inner part of Larsen B was poor in both numbers of individuals and genera, with dominance of a single Halomonhystera species. Re‐assessment of the situation in 2011 showed that communities at both stations diverged even more, due to a drastic increase in Halomonhystera at B.West compared to relatively little change at B.South. On a broader geographical scale, it seems that B.South gradually starts resembling other Antarctic shelf communities, although the absence of the genus Sabatieria and the high abundance of Microlaimus still set it apart nine years after the main Larsen B collapse. In contrast, thriving of Halomonhystera at B.West further separates its community from other Antarctic shelf areas.     

Genetic Variation for Adaptive Traits in Bottlebrush Squirreltail in the Northern Intermountain West,United States

Adaptive‐trait correlations in plant ecology are often calculated among species, but in order to develop and characterize plant materials of target species for restoration, intraspecific comparisons are of greatest relevance. Elymus elymoides (Raf.) Swezey (bottlebrush squirreltail) is an important component of sagebrush‐steppe communities in the northern Intermountain West, United States. We evaluated 32 accessions of E. elymoides subspecies C, a newly recognized unnamed taxon, in the field and greenhouse. Our objectives were to assess genetic diversity for putatively adaptive traits, to elucidate biological relationships among biomass, morphological, and phenological traits through correlation analysis, and to gather evidence suggesting whether these traits might be truly adaptive, that is, related to collection‐site variables. We observed a positive correlation (r = 0.73;p < 0.01) between greenhouse shoot and root biomass among accessions, suggesting that shoot and root biomass are not in an inherent trade‐off relationship across accessions. In addition, accessions with higher greenhouse shoot biomass possessed lower specific leaf area (r = ?0.43;p < 0.05) and lower specific root length (r = ?0.47,p < 0.05). Correlations between greenhouse and field‐measured productivity traits were not significant (p > 0.05), indicating seedling performance is not predictive of mature‐plant performance. Elevation was the collection‐site variable most closely correlated with plant‐measured traits, particularly phenological dates, whereas average annual precipitation was the least significant variable. Therefore, elevation may be used as an easily applied metric to match subspecies C plant material to restoration site in the northern Intermountain West.     

Rapid genetic delineation of local provenance seed‐collection zones for effective rehabilitation of an urban bushland remnant

Abstract The rehabilitation of native plant communities in urban bushland remnants is an increasingly important activity requiring the collection of large amounts of seed. Best practice generally identifies that local seed are best, but how far does the local provenance extend? Using the DNA fingerprinting technique amplified fragment length polymorphism, we assessed genetic differentiation between potential seed source populations and the target population, Bold Park, a large and significant bushland remnant in Perth, Western Australia. For each of 15 species, analysis of molecular variance was used to partition genetic variation within and among populations. Genetic differentiation between Bold Park and potential seed source populations was assessed by non‐metric multidimensional scaling ordination, and statistically by Fisher’s exact tests. The partitioning of variation among populations (Φ_ST) varied from 0.66 for Santalum acuminatum to 0.04 for Mesomelaena pseudostygia. For eight of 15 species, Bold Park plants were completely or largely non‐overlapping with other populations in ordinations, suggesting genetic differentiation and a narrow provenance. Five species showed overlap between Bold Park and some other, but not all, populations sampled, with geographically closest populations generally undifferentiated. Only two species, Acanthocarpus preissii and Mesomeleana pseudostygia, showed little genetic differentiation between Bold Park and all other populations, suggesting a regional genetic provenance. These species can be classified into three broad provenance classes – narrow, local and regional – to help guide decisions about appropriate seed‐collection zones for the rehabilitation of urban bushland remnants.     

Nitrogen limitation and microbial diversity at the treeline

Tree growth limitation at treeline has mainly been studied in terms of carbon limitation while effects and mechanisms of potential nitrogen (N) limitation are barely known, especially in the southern hemisphere. We investigated how soil abiotic properties and microbial community structure and composition change from lower to upper sites within three vegetation belts (Nothofagus betuloides and N. pumilio forests, and alpine vegetation) across an elevation gradient (from 0 to 650 m a.s.l.) in Cordillera Darwin, southern Patagonia. Increasing elevation was associated with a decrease in soil N‐NH₄⁺ availability within the N. pumilio and the alpine vegetation belt. Within the alpine vegetation belt, a concurrent increase in the soil C:N ratio was associated with a shift from bacterial‐dominated in lower alpine sites to fungal‐dominated microbial communities in upper alpine sites. Lower forested belts (N. betuloides, N. pumilio) exhibited more complex patterns both in terms of soil properties and microbial communities. Overall, our results concur with recent findings from high‐latitude and altitude ecosystems showing decreased nutrient availability with elevation, leading to fungal‐dominated microbial communities. We suggest that growth limitation at treeline may result, in addition to proximal climatic parameters, from a competition between trees and soil microbial communities for limited soil inorganic N. At higher elevation, soil microbial communities could have comparably greater capacities to uptake soil N than trees, and the shift towards a fungal‐dominated community would favour N immobilization over N mineralization. Though evidences of altered nutrient dynamics in tree and alpine plant tissue with increasing altitude remain needed, we contend that the measured residual low amount of inorganic N available for trees in the soil could participate to the establishment limitation. Finally, our results suggest that responses of soil microbial communities to elevation could be influenced by functional properties of forest communities for instance through variations in litter quality.     

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.     

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

Large populations of bacteria live on leaf surfaces and these phyllosphere bacteria can have important effects on plant health. However, we currently have a limited understanding of bacterial diversity on tree leaves and the inter‐ and intra‐specific variability in phyllosphere community structure. We used a barcoded pyrosequencing technique to characterize the bacterial communities from leaves of 56 tree species in Boulder, Colorado, USA, quantifying the intra‐ and inter‐individual variability in the bacterial communities from 10 of these species. We also examined the geographic variability in phyllosphere communities on Pinus ponderosa from several locations across the globe. Individual tree species harboured high levels of bacterial diversity and there was considerable variability in community composition between trees. The bacterial communities were organized in patterns predictable from the relatedness of the trees as there was significant correspondence between tree phylogeny and bacterial community phylogeny. Inter‐specific variability in bacterial community composition exceeded intra‐specific variability, a pattern that held even across continents where we observed minimal geographic differentiation in the bacterial communities on P. ponderosa needles.