Bichromatic tetraphasic full-field optical coherence microscopy.

Significance: Full-field optical coherence microscopy (FF-OCM) is a prevalent technique for backscattering and phase imaging with epi-detection. Traditional methods have two limitations: suboptimal utilization of functional information about the sample and complicated optical design with several moving parts for phase contrast. Aim: We report an OCM setup capable of generating dynamic intensity, phase, and pseudo-spectroscopic contrast with single-shot full-field video-rate imaging called bichromatic tetraphasic (BiTe) full-field OCM with no moving parts. Approach: BiTe OCM resourcefully uses the phase-shifting properties of anti-reflection (AR) coatings outside the rated bandwidths to create four unique phase shifts, which are detected with two emission filters for spectroscopic contrast. Results: BiTe OCM overcomes the disadvantages of previous FF-OCM setup techniques by capturing both the intensity and phase profiles without any artifacts or speckle noise for imaging scattering samples in three-dimensional (3D). BiTe OCM also utilizes the raw data effectively to generate three complementary contrasts: intensity, phase, and color. We demonstrate BiTe OCM to observe cellular dynamics, image live, and moving micro-animals in 3D, capture the spectroscopic hemodynamics of scattering tissues along with dynamic intensity and phase profiles, and image the microstructure of fall foliage with two different colors. Conclusions: BiTe OCM can maximize the information efficiency of FF-OCM while maintaining overall simplicity in design for quantitative, dynamic, and spectroscopic characterization of biological samples.

Effects of forest fragmentation on avian breeding activity.

Biodiversity declines and ecosystem decay follow forest fragmentation; initially, abundant species may become rare or be extirpated. Underlying mechanisms behind delayed extirpation of certain species following forest fragmentation are unknown. Species declines may be attributed to an inadequate number of breeding adults required to replace the population or decreased juvenile survival rate due to reduced recruitment or increased nest predation pressures. We used 10 years of avian banding data, 5 years before and 4 years after fragment isolation, from the Biological Dynamics of Forest Fragments Project, carried out near Manaus, Brazil, to investigate the breeding activity hypothesis that there is less breeding activity and fewer young after relative to before fragment isolation. We compared the capture rates of active breeding and young birds in 3 forest types (primary forest, fragment before isolation, and fragment after isolation) and the proportion of active breeding and young birds with all birds in each unique fragment type before and after isolation. We grouped all bird species by diet (insectivore or frugivore) and nesting strategy (open cup, cavity, or enclosed) to allow further comparisons among forest types. We found support for the breeding activity hypothesis in insectivorous and frugivorous birds (effect sizes 0.45 and 0.53, respectively) and in birds with open-cup and enclosed nesting strategies (effect sizes 0.56 and 0.44, respectively) such that on average there were more breeding birds in fragments before isolation relative to after isolation. A larger proportion of birds in the community were actively breeding before fragment isolation (72%) than after fragment isolation (11%). Unexpectedly, there was no significant decrease in the number of young birds after fragment isolation, although sample sizes for young were small (n = 43). This may have been due to sustained immigration of young birds to fragments after isolation. Together, our results provide some of the strongest evidence to date that avian breeding activity decreases in response to fragment isolation, which could be a fundamental mechanism contributing to ecosystem decay.

Efectos de la fragmentación del bosque sobre la actividad reproductiva de las aves Resumen Les declinaciones de la biodiversidad y el deterioro de los ecosistemas van después de la fragmentación forestal; al inicio, las especies abundantes pueden volverse raras o ser extirpadas. Todavía no se conocen los mecanismos subyacentes detrás de la extirpación retrasada de ciertas especies después de la fragmentación forestal. La declinación de las especies puede atribuirse a un número inadecuado de adultos reproductivos requeridos para reemplazar a la población o a la tasa reducida de supervivencia de los juveniles debido al reclutamiento disminuido o al incremento en la presión de depredación de los nidos. Usamos diez años de datos de anillamiento de aves, cinco años antes y cuatro años después del aislamiento por fragmentación, tomados del Proyecto Dinámica Biológica de Fragmentos de Bosque realizado cerca de Manaos, Brasil, para investigar la hipótesis de actividad reproductiva que sostiene que hay una menor actividad reproductiva y menos crías después del aislamiento por fragmentación que antes del aislamiento. Comparamos las tasas de captura de aves con reproducción activa y aves juveniles en tres tipos de bosque (primario, fragmento antes del aislamiento y fragmento después del aislamiento) y la proporción de las aves juveniles y con reproducción activa con todas las aves en cada tipo de fragmento único antes y después del aislamiento. Agrupamos todas las especies de aves según su dieta (insectívora o frugívora) y su estrategia de anidación (nido abierto, cavidad o nido cerrado) para poder realizar más comparaciones entre los tipos de bosque. Las aves con dieta insectívora y frugívora (tamaño del efecto: 0.45 y 0.53, respectivamente) y aquellas con nidos abiertos y cerrados (tamaño del efecto: 0.56 y 0.44, respectivamente) respaldaron la hipótesis de la actividad reproductora de tal manera que en promedio hubo más aves reproductoras en los fragmentos antes del aislamiento que después del aislamiento. Una gran parte de las aves de la comunidad tuvieron reproducción activa antes del aislamiento por fragmentación (72%) que después del aislamiento (11%). Sorprendentemente, no hubo una disminución significativa en el número de aves juveniles después del aislamiento, si bien el tamaño de la muestra de este grupo fue reducido (n = 43). Lo anterior pudo deberse a la continua inmigración de juveniles a los fragmentos después del aislamiento. En conjunto, nuestros resultados proporcionan algunos de los indicios más claros de que la actividad reproductiva de las aves disminuye como respuesta al aislamiento por fragmentación, lo cual podría ser un mecanismo fundamental del deterioro de los ecosistemas.

Sedimentary DNA for tracking the long-term changes in biodiversity.

Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.

Long-term changes in avian biomass and functional diversity within disturbed and undisturbed Amazonian rainforest.

Recent long-term studies in protected areas have revealed the loss of biodiversity, yet the ramifications for ecosystem health and resilience remain unknown. Here, we investigate how the loss of understory birds, in the lowest stratum of the forest, affects avian biomass and functional diversity in the Amazon rainforest. Across approximately 30 years in the Biological Dynamics of Forest Fragments Project, we used a historical baseline of avian communities to contrast the avian communities in today's primary forest with those in modern disturbed habitat. We found that in primary rainforest, the reduced abundance of insectivorous species led to reduced functional diversity, but no reduction of biomass, indicating that species with similar functional traits are less likely to coexist in modern primary forests. Because today's forests contain fewer functionally redundant species-those with similar traits-we argue that avian communities in modern primary Amazonian rainforests are less resilient, which may ultimately disrupt the ecosystem in dynamic and unforeseen ways.

Light and thermal niches of ground-foraging Amazonian insectivorous birds.

Insectivores of the tropical rainforest floor are consistently among the most vulnerable birds to forest clearing and fragmentation. Several hypotheses attempt to explain this pattern, including sensitivity to extreme microclimates found near forest borders, particularly brighter and warmer conditions. Importantly, this "microclimate hypothesis" has additional implications for intact forest under global climate change that could be evaluated through direct assessment of the light and temperature environment of terrestrial insectivores. In this study, we harness novel technology to directly quantify the light and thermal niches of 10 species of terrestrial insectivores in undisturbed Amazonian rainforest. Loggers placed on birds (N = 33) and their environment (N = 9) recorded nearly continuous microclimate data from 2017 to 2019, amassing >5 million measurements. We found that midday light intensity in tree fall gaps (~39,000 lux) was >40 times higher than at the ground level of forest interior (950 lux). Light intensity registered by sensors placed on birds averaged 17.4 (range 3.9-41.5) lux, with species using only 4.3% (0.9%-10.4%) of available light on the forest floor. Birds therefore selected very dark microhabitats-the light environment was >2200 times brighter in tree fall gaps. Bird thermal niche was a function of ambient temperature as well as body temperature, which averaged >40.5°C but varied among species. Forest floor temperature peaked daily at 27.0°C, whereas bird loggers averaged 35.1°C (34.5-35.7°C) at midday. The antpitta Myrmothera campanisona and the antthrush Formicarius colma used thermal conditions closest to their body temperatures, whereas leaftossers (Sclerurus spp.) and Myrmornis torquata occupied relatively cool microclimates. We found no general link between abundance trends and variation in species-specific light and thermal niches. However, all species occupied markedly dim and cool microclimates. Because such conditions are rare outside the interior of primary forest, these results support the microclimate hypothesis in disturbed landscapes. Moreover, strong avoidance of conditions that are becoming more common under climate change highlights the vulnerability of terrestrial insectivores even in the absence of disturbance and may be the reason for enigmatic declines in Amazonia and elsewhere.

Long-term change in the avifauna of undisturbed Amazonian rainforest: ground-foraging birds disappear and the baseline shifts.

How are rainforest birds faring in the Anthropocene? We use bird captures spanning > 35 years from 55 sites within a vast area of intact Amazonian rainforest to reveal reduced abundance of terrestrial and near-ground insectivores in the absence of deforestation, edge effects or other direct anthropogenic landscape change. Because undisturbed forest includes far fewer terrestrial and near-ground insectivores than it did historically, today's fragments and second growth are more impoverished than shown by comparisons with modern 'control' sites. Any goals for bird community recovery in Amazonian second growth should recognise that a modern bird community will inevitably differ from a baseline from > 35 years ago. Abundance patterns driven by landscape change may be the most conspicuous manifestation of human activity, but biodiversity declines in undisturbed forest represent hidden losses, possibly driven by climate change, that may be pervasive in intact Amazonian forests and other systems considered to be undisturbed.

The Maximum Caliber Variational Principle for Nonequilibria.

Ever since Clausius in 1865 and Boltzmann in 1877, the concepts of entropy and of its maximization have been the foundations for predicting how material equilibria derive from microscopic properties. But, despite much work, there has been no equally satisfactory general variational principle for nonequilibrium situations. However, in 1980, a new avenue was opened by E.T. Jaynes and by Shore and Johnson. We review here maximum caliber, which is a maximum-entropy-like principle that can infer distributions of flows over pathways, given dynamical constraints. This approach is providing new insights, particularly into few-particle complex systems, such as gene circuits, protein conformational reaction coordinates, network traffic, bird flocking, cell motility, and neuronal firing.

New Schemes of Dynamic Preservation of Diversity: Remarks on Stability and Topology.

We address the biological dynamics problem of the persistence of several species in conditions of non-existence of an equilibrium, including an example of stabilization by predation and the very controversial "competitive exclusion" (which depends on the precise definition of persistence). We give normal forms for various examples of such (essentially dynamical) persistence and comments on the involved topology, which implies the presence of exceptional heteroclinic connections binding equilibria on the boundary.

Single-Molecule Nanotechnologies: An Evolution in Biological Dynamics Detection.

Single-molecule detection is a rapidly developing area within the analytical chemistry field that requires ultrasensitive technologies to detect a range of molecules. Over the past few decades, various optically-, mechanically-, and electrically-based strategies have been employed for single-molecule detection to uncover information in biological processes. These strategies enable real-time monitoring with single-molecule/single-event sensitivity. In addition, their high temporal resolution enables investigation of the underlying mechanisms of biological functions from static to dynamic, from qualitative to quantitative, and from one to multiple disciplines. In this review, we provide a brief overview of the prominent, real-time single-molecule detection nanotechnologies and their potential applications within the life science fields.

Amazonian trees show increased edge effects due to Atlantic Ocean warming and northward displacement of the Intertropical Convergence Zone since 1980.

Recent investigations indicate a warming of Atlantic Ocean surface waters since 1980, probably influenced by anthropic actions, inducing rainfall intensification mainly during the rainy season and slight reductions during the dry season in the Amazon. Under these climate changes, trees in upland forests (terra firme) could benefit from the intensification of the hydrological cycle and could also be affected by the reduction of precipitation during the dry season. Results of dendrochronological analyses, spatial correlations and structural equation models, showed that Scleronema micranthum (Ducke) Ducke (Malvaceae) trees exposed in fragmented areas and to edge effects in Central Amazonian terra firme forest were more sensitive to the increase in the Atlantic Ocean surface temperature and consequent northward displacement of the Intertropical Convergence Zone, mainly during the dry season. Therefore, we proved that in altered and potentially more stressful environments such as edges of fragmented forests, recent anthropogenic climatic changes are exerting pressure on tree growth dynamics, inducing alterations in their performance and, consequently, in essential processes related to ecosystem services. Changes that could affect human well-being, highlighting the need for strategies that reduce edge areas expansion in Amazon forests and anthropic climate changes of the Anthropocene.

Persistent effects of fragmentation on tropical rainforest canopy structure after 20 yr of isolation.

Assessing the persistent impacts of fragmentation on aboveground structure of tropical forests is essential to understanding the consequences of land use change for carbon storage and other ecosystem functions. We investigated the influence of edge distance and fragment size on canopy structure, aboveground woody biomass (AGB), and AGB turnover in the Biological Dynamics of Forest Fragments Project (BDFFP) in central Amazon, Brazil, after 22+ yr of fragment isolation, by combining canopy variables collected with portable canopy profiling lidar and airborne laser scanning surveys with long-term forest inventories. Forest height decreased by 30% at edges of large fragments (>10 ha) and interiors of small fragments (<3 ha). In larger fragments, canopy height was reduced up to 40 m from edges. Leaf area density profiles differed near edges: the density of understory vegetation was higher and midstory vegetation lower, consistent with canopy reorganization via increased regeneration of pioneers following post-fragmentation mortality of large trees. However, canopy openness and leaf area index remained similar to control plots throughout fragments, while canopy spatial heterogeneity was generally lower at edges. AGB stocks and fluxes were positively related to canopy height and negatively related to spatial heterogeneity. Other forest structure variables typically used to assess the ecological impacts of fragmentation (basal area, density of individuals, and density of pioneer trees) were also related to lidar-derived canopy surface variables. Canopy reorganization through the replacement of edge-sensitive species by disturbance-tolerant ones may have mitigated the biomass loss effects due to fragmentation observed in the earlier years of BDFFP. Lidar technology offered novel insights and observational scales for analysis of the ecological impacts of fragmentation on forest structure and function, specifically aboveground biomass storage.

Nitrate denitrification with nitrite or nitrous oxide as intermediate products: Stoichiometry, kinetics and dynamics of stable isotope signatures.

A kinetic analysis of nitrate denitrification by a single or two species of denitrifying bacteria with glucose or ethanol as a carbon source and nitrite or nitrous oxide as intermediate products was performed using experimental data published earlier (Menyailo and Hungate, 2006; Vidal-Gavilan et al., 2013). Modified Monod kinetics was used in the dynamic biological model. The special equations were added to the common dynamic biological model to describe how isotopic fractionation between N species changes. In contrast to the generally assumed first-order kinetics, in this paper, the traditional Rayleigh equation describing stable nitrogen and oxygen isotope fractionation in nitrate was derived from the dynamic isotopic equations for any type of kinetics. In accordance with the model, in Vidal-Gavilan's experiments, the maximum specific rate of nitrate reduction was proved to be less for ethanol compared to glucose. Conversely, the maximum specific rate of nitrite reduction was proved to be much less for glucose compared to ethanol. Thus, the intermediate nitrite concentration was negligible for the ethanol experiment, while it was significant for the glucose experiment. In Menyailo's and Hungate's experiments, the low value of maximum specific rate of nitrous oxide reduction gives high intermediate value of nitrous oxide concentration. The model showed that the dynamics of nitrogen and oxygen isotope signatures are responding to the biological dynamics. Two microbial species instead of single denitrifying bacteria are proved to be more adequate to describe the total process of nitrate denitrification to dinitrogen.