Leaf and Soil Nutrients in a Chronosequence of Second‐Growth Forest in Central Amazonia: Implications for Restoration of Abandoned Lands

Subsistence agriculture, cattle ranching, and periodical land abandonment are common land‐use practices in Amazonia. Because changes in land use affect biogeochemical cycles, secondary forests growing after land abandonment develop at varying speeds and spatial patterns, due in part to varying nutrient dynamics. Leaf and soil nutrient concentrations can provide useful information on nutrient cycling processes and strategies of nutrient use by trees that are suitable for introduction to abandoned areas. To understand nutrient dynamics in secondary forests from different regeneration stages, as well as the importance of pioneer species in the regeneration process, we measured the concentration of macronutrients in leaves of three pioneer tree species (Vismia cayennensis, Cecropia sciadophylla, and Bellucia dichotoma) in central Amazon secondary forests. We also measured macronutrients in the topsoil under the trees. We found that type of prior land use, time since abandonment, and number of fire events were significantly correlated with the concentrations of leaf and soil macronutrients, explaining between 10 and 38% of the variation in macronutrient concentrations. The observed patterns suggest that management practices affect the processes involved in N cycling and availability. Of the three pioneer species, C. sciadophylla showed the highest nutrient resorption efficiency and the highest leaf nutritional quality. We suggest that these two features determine a higher potential of C. sciadophylla for natural regeneration and restoration of abandoned lands.     

Multi‐stage disruption of freshwater mussel reproduction by high suspended solids in short‐ and long‐term brooders

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Diameter Growth of Juvenile Trees after Gap Formation in a Bolivian Rain Forest: Responses are Strongly Species‐specific and Size‐dependent

We evaluated growth responses to gap formation for juvenile individuals of three canopy rain forest species: Peltogyne cf. heterophylla, Clarisia racemosa and Cedrelinga catenaeformis. Gaps were formed during selective logging operations 7 yr before sampling in a Bolivian rain forest. We collected wood samples for tree‐ring analyses at different distances to the stump (<10, 10–40 and >40 m) and from trees with different diameters (5–30 cm diameter at breast height [dbh]). Tree‐rings width was measured in at least two radii and converted to average diameter growth. Changes in 7‐yr median diameter growth before and after selective logging were analyzed. Diameter growth rates significantly increased by 0.7–0.8 mm/yr after gap formation for P. heterophylla and C. catenaeformis, but not for C. racemosa. We applied a multiple regression analysis to explain variation in growth responses of P. heterophylla and C. catenaeformis by distance to logging gap and tree size. For P. heterophylla we found that growth increase occurring close to logging gaps was strongest for large juvenile trees (20–25 cm dbh) and almost absent in small juveniles. For C. catenaeformis, variation in growth responses was not related to tree size or distance to gaps. Our results show that growth responses to gap formation strongly differ across species and tree sizes. This finding calls for caution in the interpretation of growth releases in tree‐ring series, as gap formation does not necessarily invoke growth responses and if such growth responses occur, their strength is species‐ and size specific.     

ADAM12‐deficient zebrafish exhibit retardation in body growth at the juvenile stage without developmental defects

ADAM (a d isintegrin a nd m etalloprotease) constitutes a family of multi‐domain proteins that are involved in development, homeostasis, and disease. ADAM12 plays important roles in myogenesis and adipogenesis in mice; however, the precise physiological mechanisms are not known, and the function of this gene in other vertebrates has not been examined. In this study, we used a simple model vertebrate, the zebrafish, to investigate the functions of ADAM12 during development. Zebrafish adam12 is conserved with those of mammals in the synteny and the amino‐acid sequence. We examined adam12 expression in zebrafish embryos by whole mount in situ hybridization and the promoter activity of the adam12 upstream sequence. We found that adam12 is strongly expressed in the cardiovascular system, erythroid progenitors, brain, and jaw cartilage during zebrafish development, and adam12‐knockout zebrafish exhibited reduced body size in the juvenile stage without apparent morphological defects. Taken together, these results suggest that adam12 plays a significant role in the regulation of body growth during juvenile stage in zebrafish, although the precise molecular mechanisms await further study.     

Black Bear Reactions to Venomous and Non‐venomous Snakes in Eastern North America

Bears are often considered ecological equivalents of large primates, but the latter often respond with fear, avoidance, and alarm calls to snakes, both venomous and non‐venomous, there is sparse information on how bears respond to snakes. We videotaped or directly observed natural encounters between black bears (Ursus americanus) and snakes. Inside the range of venomous snakes in Arkansas and West Virginia, adolescent and adult black bears reacted fearfully in seven of seven encounters upon becoming aware of venomous and non‐venomous snakes; but in northern Michigan and Minnesota where venomous snakes have been absent for millennia, black bears showed little or no fear in four encounters with non‐venomous snakes of three species. The possible roles of experience and evolution in bear reactions to snakes and vice versa are discussed. In all areas studied, black bears had difficulty to recognize non‐moving snakes by smell or sight. Bears did not react until snakes moved in 11 of 12 encounters with non‐moving timber rattlesnakes (Crotalus horridus) and four species of harmless snakes. However, in additional tests in this study, bears were repulsed by garter snakes that had excreted pungent anal exudates, which may help explain the absence of snakes, both venomous and harmless, in bear diets reported to date.     

Protocols for Use of Potamogeton perfoliatus and Ruppia maritima Seeds in Large‐Scale Restoration

Restoration of submerged aquatic vegetation from seed has been hampered by a lack of information on the appropriate conditions for collecting, processing, and storing seeds prior to dispersal. Seeds must be processed and stored under conditions that maintain seed viability, meet dormancy requirements, and prevent premature germination. This study examined the effects of collection date, processing technique, aeration, storage and induction temperature and salinity, and storage period on seed germination of two mesohaline aquatic species, Potamogeton perfoliatus and Ruppia maritima. Collection date and processing technique were significant factors affecting seed yield from donor populations. Seeds of both species remained viable and germinated best when stored at 4°C, and then exposed to freshwater induction conditions. However, their responses to other factors differed. Aeration during storage was necessary in order to maintain viability of P. perfoliatus seeds, whereas it was unnecessary for R. maritima seeds. Storage in freshwater at 4°C prevented germination of P. perfoliatus seeds, while high salinity during cold storage was necessary to minimize premature germination of R. maritima. Mean germination time of P. perfoliatus was dependent on storage salinity; in contrast, mean germination time of R. maritima seeds was dependent on induction salinity. These differences indicate that the methods required to produce large quantities of underwater plant seed amenable to large‐scale restoration efforts must be tailored to the specific requirements of individual species and must consider the range of processes from initial harvest through seed testing prior to field establishment.     

Rehabilitation of a Bauxite Tailing Substrate in Central Amazonia: The Effect of Litter and Seed Addition on Flood‐Prone Forest Restoration

Impacts of mining activity can be particularly difficult to remediate in wetland ecosystems subject to inundation pulses due to the reduced length of the plant growing season. We used a factorial experiment to test whether litter and seed addition could be used to increase the efficiency of ecological restoration on a flood‐prone forest (known as igapó) impacted by deposition of bauxite tailings. Our results clearly showed that the addition of litter collected from pristine igapó areas increased plant growth, seedling density, and seedling species richness. The increase in individual plant growth was echoed at the community level with higher leaf area index values on litter addition plots compared to controls. Litter addition can enhance reaccumulation of nutrient pools during successional development, which has been proposed as an important feature to ensure self‐sustainability of areas under restoration. The success of the seed addition treatment depended on the species used. Of the seven sown species, only Acosmium nitens (a leguminous nitrogen‐fixing species) showed high establishment. The introduction of nitrogen‐fixing species is also expected to build up the nitrogen pool in the system as has been reported for restoration programs in non‐inundated forests. These practices have the advantage, compared to direct fertilizing, of not causing eutrophication of water bodies when applied to flood‐prone vegetation.     

Effect of culturing parameters on the vegetative growth of Haematococcus alpinus (strain lcr‐cc‐261f) and modeling of its growth kinetics

The present study investigated the effect of different culture conditions on the vegetative growth of a new species, Haematococcus alpinus (strain LCR‐CC‐261f) using airlift photobioreactors. The influence of culture medium, aeration rates, CO₂ concentration in air‐gas mixture, temperature, light intensities, and wavelengths were investigated to achieve sustainable high cell density cultures. Growth parameters were determined by fitting the data to a form of the logistic equation that included a lag phase. The shear‐sensitive vegetative cells favored lower aeration rates in the photobioreactors. MLA medium increased to 40 mM nitrate produced high density cultures. Temperatures between 12°C and 18°C, 3% (v/v) CO₂ concentration and a narrow photon flux density ranging between 37 and 48 μmol photons · m^?2 · s^?1 were best suited for growth. The wavelength of the light source also impacted growth and a high cell density of 9.6 × 10⁵ cells · mL^?1 was achieved using a mixture of red and blue compared to warm white, red, or blue LEDs.     

High‐resolution time‐resolved imaging of in vitro Arabidopsis rosette growth

Although quantitative characterization of growth phenotypes is of key importance for the understanding of essential networks driving plant growth, the majority of growth‐related genes are still being identified based on qualitative visual observations and/or single‐endpoint quantitative measurements. We developed an in vitro growth imaging system (IGIS) to perform time‐resolved analysis of rosette growth. In this system, Arabidopsis plants are grown in Petri dishes mounted on a rotating disk, and images of each plate are taken on an hourly basis. Automated image analysis was developed in order to obtain several growth‐related parameters, such as projected rosette area, rosette relative growth rate, compactness and stockiness, over time. To illustrate the use of the platform and the resulting data, we present the results for the growth response of Col–0 plants subjected to three mild stress conditions. Although the reduction in rosette area was relatively similar at 19 days after stratification, the time‐lapse analysis demonstrated that plants react differently to salt, osmotic and oxidative stress. The rosette area was altered at various time points during development, and leaf movement and shape parameters were also affected differently. We also used the IGIS to analyze in detail the growth behavior of mutants with enhanced leaf size. Analysis of several growth‐related parameters over time in these mutants revealed several specificities in growth behavior, underlining the high complexity of leaf growth coordination. These results demonstrate that time‐resolved imaging of in vitro rosette growth generates a better understanding of growth phenotypes than endpoint measurements.     

Half a century of Scots pine forest ecosystem monitoring reveals long‐term effects of atmospheric deposition and climate change

At two forest sites in Germany (Pfaffenwinkel, Pustert) stocked with mature Scots pine (Pinus sylvestris L.), we investigated changes of topsoil chemistry during the recent 40 years by soil inventories conducted on replicated control plots of fertilization experiments, allowing a statistical analysis. Additionally, we monitored the nutritional status of both stands from 1964 until 2019 and quantified stand growth during the monitoring period by repeated stand inventories. Moreover, we monitored climate variables (air temperature and precipitation) and calculated annual climatic water balances from 1991 to 2019. Atmospheric nitrogen (N) and sulfur (S) deposition between 1964 and 2019 was estimated for the period 1969–2019 by combining annual deposition measurements conducted in 1985–1987 and 2004 with long‐term deposition records from long‐term forest monitoring stations. We investigated interrelations between topsoil chemistry, stand nutrition, stand growth, deposition, and climate trends. At both sites, the onset of the new millennium was a turning point of important biogeochemical processes. Topsoil acidification turned into re‐alkalinization, soil organic matter (SOM) accumulation stopped, and likely turned into SOM depletion. In the new millennium, topsoil stocks of S and plant‐available phosphorus (P) as well as S and P concentrations in Scots pine foliage decreased substantially; yet, age‐referenced stand growth remained at levels far above those expected from yield table data. Tree P and S nutrition as well as climate change (increased temperature and drought stress) have replaced soil acidification as major future challenges for both forests. Understanding of P and S cycling and water fluxes in forest ecosystems, and consideration of these issues in forest management is important for successfully tackling the new challenges. Our study illustrates the importance of long‐term forest monitoring to identify slow, but substantial changes of forest biogeochemistry driven by natural and anthropogenic global change.     

Landscape‐scale Variation in Pathogen‐suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica

Bacteria in the genus Streptomyces are ubiquitous in soil and are well‐known for their production of diverse secondary metabolites, including antibiotics that can inhibit soil‐borne plant pathogens and suppress disease. Pathogen‐suppressive soil bacteria have the potential to influence plant community composition and diversity, but remain relatively unexplored in tropical forest soils. To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil‐borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde) and quantified antibiotic‐mediated pathogen inhibition against three plant pathogens. The potential for pathogen inhibition and disease suppression by Streptomyces was highly variable across the landscape. Densities of pathogen‐suppressive Streptomyces varied by over ten‐fold and were correlated with soil nutrients across the plots. In particular, Streptomyces communities became more pathogen‐suppressive as labile soil P decreased. Inhibitor densities were significantly higher in Santa Rosa than Palo Verde, which may be related to differences in soil texture and/or plant community composition between the two forests. Our findings suggest potential differences in the degree and specificity of antibiotic‐mediated disease suppression in tropical dry forest soils of Costa Rica, and highlight the need for further studies on the drivers of pathogen‐suppressive phenotypes as well as the consequences of spatially variable pathogen inhibition for plant community composition in tropical forest ecosystems.     

Nonlinear effects of climate on boreal rodent dynamics: mild winters do not negate high‐amplitude cycles

Small rodents are key species in many ecosystems. In boreal and subarctic environments, their importance is heightened by pronounced multiannual population cycles. Alarmingly, the previously regular rodent cycles appear to be collapsing simultaneously in many areas. Climate change, particularly decreasing snow quality or quantity in winter, is hypothesized as a causal factor, but the evidence is contradictory. Reliable analysis of population dynamics and the influence of climate thereon necessitate spatially and temporally extensive data. We combined data on vole abundances and climate, collected at 33 locations throughout Finland from 1970 to 2011, to test the hypothesis that warming winters are causing a disappearance of multiannual vole cycles. We predicted that vole population dynamics exhibit geographic and temporal variation associated with variation in climate; reduced cyclicity should be observed when and where winter weather has become milder. We found that the temporal patterns in cyclicity varied between climatically different regions: a transient reduction in cycle amplitude in the coldest region, low‐amplitude cycles or irregular dynamics in the climatically intermediate regions, and strengthening cyclicity in the warmest region. Our results did not support the hypothesis that mild winters are uniformly leading to irregular dynamics in boreal vole populations. Long and cold winters were neither a prerequisite for high‐amplitude multiannual cycles, nor were mild winters with reduced snow cover associated with reduced winter growth rates. Population dynamics correlated more strongly with growing season than with winter conditions. Cyclicity was weakened by increasing growing season temperatures in the cold, but strengthened in the warm regions. High‐amplitude multiannual vole cycles emerge in two climatic regimes: a winter‐driven cycle in cold, and a summer‐driven cycle in warm climates. Finally, we show that geographic climatic gradients alone may not reliably predict biological responses to climate change.     

Sequence‐tagged high‐density genetic maps of Zoysia japonica provide insights into genome evolution in Chloridoideae

Zoysiagrass (Zoysia spp.), belonging to the genus Zoysia in the subfamily Chloridoideae, is widely used in domestic lawns, sports fields and as forage. We constructed high‐density genetic maps of Zoysia japonica using a restriction site‐associated DNA sequencing (RAD‐Seq) approach and an F₁ mapping population derived from a cross between ‘Carrizo’ and ‘El Toro’. Two linkage maps were constructed, one for each of the parents. A map consisting of 2408 RAD markers distributed on 21 linkage groups was constructed for ‘Carrizo’. Another map with 1230 RAD markers mapped on 20 linkage groups was constructed for ‘El Toro’. The average distance between adjacent markers of the two maps was at 0.56 and 1.4 cM, respectively. Comparative genomics analysis was carried out among zoysiagrass, rice and sorghum genomes and a highly conserved collinearity in the gene order was observed among the three genomes. Chromosome collinearity was disrupted at centromeric regions for each chromosome pair between zoysiagrass and sorghum genomes. However, no obvious synteny gaps were observed across the centromeric regions between zoysiagrass and rice genomes. Two homologous chromosomes for each of the 10 sorghum chromosomes were found in the zoysiagrass genome, indicating an allotetraploid origin for zoysiagrass. The reduction of the basic chromosome number from 12 to 10 in chloridoids and panicoids took place via independent single‐step nested chromosome fusion events after the two subfamilies diverged from a common ancestor. The genetic maps will assist in genome sequence assembly, targeted gene isolation and comparative genomic analyses among grasses.     

Impacts of nitrogen fertilizer on major insect pests and their predators in transgenic Bt rice lines T2A‐1 and T1C‐19

Nitrogen is a critical factor for plant development and nitrogen input is one of the important tactics to enhance the development and yield of crops. Nevertheless, nitrogen input could influence the occurrence of insects positively or negatively. Nitrogen is also one of the main elements composing the insecticidal crystal (Cry) protein. Cry protein production could affect nitrogen partitioning in Bt plants and as such nitrogen input may influence insect pest management in transgenic Bt rice, Oryza sativa L. (Poaceae). To test this possibility, we evaluated the impacts of nitrogen regimes on the main insect pests and their predators on two Bt rice lines, T2A‐1 and T1C‐19, expressing Cry2A and Cry1C, respectively, and their non‐transgenic parental counterpart MH63. The results showed that Cry proteins with different nitrogen regimes have enough insecticidal activity on rice leaffolder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Crambidae), in both laboratory and field experiments. Laboratory studies indicated that relevant parameters of ecological fitness in brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), a non‐target insect pest, were significantly affected by nitrogen input both on Bt and MH63 rice lines. Nymphal survival, female adult longevity, and egg hatchability in N. lugens differed significantly among rice varieties. The experiments conducted in rice fields also demonstrated that nitrogen was positively correlated with the abundance of N. lugens on Bt rice, similar to that on MH63 rice. The abundances of two predators – the wolf spider Pirata subpiraticus (Boesenberg & Strand) (Araneae: Lycosidae) and the bug Cyrthorhinus lividipennis Reuter (Hemiptera: Miridae) – were significantly affected by rice growth stages but not by nitrogen input and rice varieties. In conclusion, the above results indicate that high nitrogen regimes for Bt rice (T2A‐1 and T1C‐19) and non‐Bt rice (MH63) cannot facilitate the management of insect pests.     

Alteration and Recovery of Slash Pile Burn Sites in the Restoration of a Fire‐Maintained Ecosystem

Restoration practices incorporating timber harvest (e.g. to remove undesirable species or reduce tree densities) may generate unmerchantable wood debris that is piled and burned for fuel reduction. Slash pile burns are common in longleaf pine ecosystem restoration that involves hardwood removal before reintroduction of frequent prescribed fire. In this context, long‐lasting effects of slash pile burns may complicate restoration outcomes due to unintended alterations to vegetation, soils, and the soil seed bank. In this study, our objectives were to (1) examine alterations to the soil seed bank, soil physical and chemical characteristics, and initial vegetation recolonization following burn and (2) determine the rate of return of soil and vegetation characteristics to pre‐burn conditions. We found that burning of slash piles (composed of scores of whole trees) results in elevated nutrient levels and significant impacts on vegetation and the soil seed bank, which remain evident for at least 6 years following burn. In this ecosystem, formerly weakly acidic soils become neutral to basic and levels of P remain significantly higher. Following an initial decrease after burn, total soil N increases with time since burn. These changes suggest that not only does pile burning create a fire scar initially devoid of biota, but it also produces an altered soil chemical environment, with possible consequences for long‐term ecosystem restoration efforts in landscapes including numerous fire scars. To facilitate restoration trajectories, further adaptive management to incorporate native plant propagules or suppress encroaching hardwoods within fire scars may be warranted in fire‐dependent ecosystems.     

Nitrogen‐dependent bacterial community shifts in root,rhizome and rhizosphere of nutrient‐efficient Miscanthus x giganteus from long‐term field trials

The perennial energy crop Miscanthus × giganteus is recognized for its extraordinary nitrogen‐use efficiency. While the remobilization of nitrogen (N) to the rhizome after the growth phase contributes to this efficiency, the plant‐associated microbiome might also contribute, as N‐fixing bacterial species had been isolated from this grass. Here, we studied established Miscanthus × giganteus plots in southern Germany that either received 80 kg N ha^?1 a^?1 or that were not N‐fertilized for 14 years. The bacterial communities of the bulk soil, rhizosphere, roots and rhizomes were analysed. Major differences were encountered between plant‐associated fractions. Nitrogen had little effect on soil communities. The roots and rhizomes showed less microbial diversity than soil fractions. In these compartments, Actinobacteria and N‐fixing symbiosis‐associated Proteobacteria depended on N. Intriguingly, N₂‐fixing‐related bacterial families were enriched in the rhizomes in long‐term zero N plots, while denitrifier‐related families were depleted. These findings point to the rhizome as a potentially interesting plant organ for N fixation and demonstrate long‐term differences in the organ‐specific bacterial communities associated with different N supply, which are mainly shaped by the plant.     

Trophic Niche Differentiation and Microhabitat Utilization in a Species‐rich Montane Forest Small Mammal Community of Eastern Madagascar

Unraveling the mechanisms facilitating species coexistence in communities is a central theme in ecology. Species‐rich tropical mammal communities provide excellent settings to explore such mechanisms as they often harbor numerous congeneric species with close phylogenetic relationships. Explicit tests for the mechanisms that allow syntopic occurrence in these assemblages, however, is often hampered because of the difficulty in obtaining detailed ecological data on the organisms making up the community. Using stable nitrogen and carbon ratios of hair samples, we examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 21 small mammal species at a montane humid forest site in eastern Madagascar. Overall, the community was trophically diverse and covered wide isotopic space. This diversity was based on: (1) a multi‐layered trophic community structure with mainly frugivorous‐granivorous rodents (subfamily Nesomyinae) as primary consumers and insectivorous tenrecs (family Tenrecidae) as secondary and tertiary consumers; (2) trophic segregation of rodents and tenrecs with the latter occupying different microhabitats; and (3) a dense and regular packing of species in the community. The 12 locally occurring Microgale shrew tenrecs (subfamily Oryzorictinae) showed high trophic redundancy, but were maximally spaced from each other within the trophic space covered by the genus. Results of stable isotope analysis suggest that in combination the differentiation of microhabitats and trophic niches explain the coexistence of small mammals in this community. Congeneric species appeared to be under more intense competition compared with non‐congeneric species and their coexistence can only partly be explained by trophic and microhabitat niche segregation.     

Experimental demonstration of accelerated extinction in source‐sink metapopulations

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source‐sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source‐sink effects in laboratory populations of Daphnia magna. Time‐to‐extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source‐sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.