PORQUE O MUNDO É VERDE, AS ÁGUAS AZUIS E OS PEQUENOS RIOS DA MATA ATLÂNTICA SÃO ALIMENTADOS PRINCIPALMENTE POR MICROALGAS?

The question “Why is the world green?” has been debated and researched ever since the seminal paper of Hairston et al. (1960). Three main hypotheses were generated to explain why a large part of terrestrial plant biomass is not eaten by herbivores: (1) predators control herbivores (especially folivores), (2) plant defenses inhibit herbivores, and render the plant biomass relatively unavailable, and (3) different controls operate in regions of different productivity. Aquatic systems, especially those of plankton, tend to have much less plant biomass than terrestrial systems, and generally a much higher proportion of the living plant biomass is consumed by herbivores. Thus open-water aquatic systems appear transparent blue or green. They also often display cascading relationships in which changes at one trophic level have effects at two or more levels below. The orthodoxy for small streams shaded by forest is that they receive much organic matter from the surrounding forest and this provides the main source of energy and material for the food web. Some recent search in tropical streams shows that microalgae provide a greater proportion of the primary source than does allochthonous material. This may be a specifically tropical phenomenon, or perhaps a tendency that is more accentuated in the tropics. Exclusion experiments show trophic cascades and strong interactions between fauna (particularly shrimps) and allochthonous substrates. But the functional interactions (shredding of litter, removal of benthic material) are not trophic -- the animals are herbivores or predators of herbivores based on microalgae. We can speculate that the apparent wastage of allochthonous material is at least partly due to the inherent costs that a detritivore would have in processing the more intractable and less nutritive food source (litter) in conditions of higher predation and competition, which are possibly more stringent in the tropics.A questão “Porque o mundo é verde?” tem sido debatida e pesquisada desde a publicação seminal de Hairston et al. (1960). Três principais hipóteses foram levantadas para explicar porque uma grande parte da biomassa de plantas terrestres não é comida por herbívoros: (1) predadores controlam herbívoros (especialmente folívoros), (2) defesas das plantas inibem herbívoros e tornam a biomassa relativamente não disponível e, (3) diferentes controles operam em regiões com produtividades diferentes. Sistemas aquáticos, especialmente os de plâncton, tendem a ter muito menos biomassa de plantas que sistemas terrestres e, geralmente, uma porção bem maior da biomassa viva é consumida por herbívoros. Daí sistemas de águas abertas parecerem azul ou verde transparente. Tais sistemas muitas vezes mostram relações em cascata nas quais as mudanças em um nível trófico têm efeitos em dois ou mais níveis abaixo. A regra geral em pequenos rios sombreados de floresta é que recebam muita matéria orgânica proveniente da floresta ao redor, e isto fornece a fonte principal de energia e material para a rede trófica. Pesquisas recentes em pequenos rios tropicais mostram que microalgas fornecem uma parte maior da fonte primária do que a matéria alóctone. Isto pode ser um fenômeno especificamente tropical, ou talvez uma tendência, mais acentuada nos trópicos. Experimentos de exclusão mostram cascatas tróficas e interações fortes entre fauna (especialmente camarões) e substrato alóctone. Mas as interações funcionais (e.g., rasgar serapilheira, remover matéria bêntica) não são tróficas -- os animais são herbívoros ou predadores de herbívoros baseados em microalgas. Podemos especular que o desperdício aparente de matéria alóctone se deva em parte aos custos inerentes que o detritívoro teria que arcar por processar uma fonte menos tratável e menos nutritiva (serapilheira) em condições de predação e competição maiores, que possivelmente são mais exigentes nos trópicos

APLICANDO PESQUISAS PARA CONSERVAÇÃO NO PARQUE ESTADUAL DA ILHA DO CARDOSO, SP

Na Ilha do Cardoso nós temos uma ótima oportunidade de aplicar pesquisa para conservação de um importante espectro de ambientes - Mata Atlântica, restinga, manguezal, estuário, praias e costões rochosos - e preservar sua flora e fauna. O Centro de Pesquisa situado na Ilha do Cardoso, CEPARNIC, dedica-se a aplicar pesquisa para o planejamento e manejo do Parque Estadual, e para a conservação da região como um todo. Os modelos gerados no CEPARN IC devem ter um largo espectro de implicações, de modelos gerais a como pesquisa pode ser aplicada a problemas práticos em parques, até modelos de funcionamento de ecossistema e manutenção da diversidade. Para que estes objetivos sejam alcançados, é essencial que o trabalho seja integrado a níveis mais altos de organização - planejamento, conservação, ecossistemas, etc. Apresento aqui uma proposta de como isto pode ser organizado e discuto a teoria e a prática de como fazê10. O esquema segue essencialmente os princípios de análise de sistema: modelos são montados definindo os objetivos e como os sistemas devem funcionar e isto orienta a pesquisa que é conduzida no nível básico (botânico, zoológico e ecológico). Em troca, os resultados da pesquisa são reaplicados aos modelos e servem para refiná-Ios e gerar mais hipóteses. O CEPARNIC é obviamente a instituição que deve ter o papel de coordenação e a pesquisa vem de projetos passados, presentes e futuros, das muitas instituições e universidades que usam as instalações do CEPARNIC

Conservation of catchments: some theoretical considerations and case histories from Rio de Janeiro

Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management.Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management

Conservation of catchments: some theoretical considerations and case histories from Rio de Janeiro

Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management.Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds

<p>Abstract</p> <p>Background</p> <p>The computational identification of RNAs in genomic sequences requires the identification of signals of RNA sequences. Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs). Under the Boltzmann ensemble of secondary structures, the probability of a base pair is estimated from its frequency across all the alternative equilibrium structures. However, such an entropy has yet to deliver the desired performance for distinguishing ncRNAs from random sequences. Developing novel methods to improve the entropy measure performance may result in more effective ncRNA gene finding based on structure detection.</p> <p>Results</p> <p>This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed to occur in energetically stable stems in a fold. This constraint actually reduces the space of the secondary structure and may lower the probabilities of base pairs unfavorable to the native fold. Indeed, base pairing entropies computed with this constrained model demonstrate substantially narrowed gaps of Z-scores between ncRNAs, as well as drastic increases in the Z-score for all 13 tested ncRNA sets, compared to shuffled sequences.</p> <p>Conclusions</p> <p>These results suggest the viability of developing effective structure-based ncRNA gene finding methods by investigating secondary structure ensembles of ncRNAs.</p

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change

Relationships of shredders, leaf processing and organic matter along a canopy cover gradient in tropical streams

Terrestrial allochthonous organic matter represents a structuring element and an important source of energy and carbon to fauna in small forested streams. However, the role of this matter as a food resource for benthic macroinvertebrates, and consequently, for shredders and their performance in riverine processes, is not clear in low-order tropical streams. Aiming to investigate the relationship between shredders and leaves, we analyzed along a gradient of 8-93% canopy cover biomass and abundance of shredders, accumulated leaves and breakdown rates of local leaves to verify if these parameters were related to shade conditions and to each other. Three hypotheses were tested: i) shredder biomass, accumulated leaves and breakdown rates are related to canopy cover and exhibit higher values in shaded sites; ii) shredder biomass is positively related to accumulated leaves and breakdown rates; and iii) due to the relatively large body size of the important shredders, the association of shredders with leaves and importance to leaf processing should be better expressed in terms of guild biomass than abundance. Shredder biomass varied between 846 and 1506 mg DM m‑2 and accumulated leaves varied between 479 and 1120 g AFDM m-2 across sites. Leaf breakdown rate (k), the only measured variable that varied significantly among sites, varied between -0.0015 and -0.0238 day-1. Neither shredder biomass nor leaf biomass were associated with the shading gradient.  On the other hand, shredder abundance and biomass, mainly represented by Triplectides (Trichoptera, Leptoceridae), was positively related to accumulated leaves within sites and to breakdown rates assessed by leaf packs. Leaf breakdown, as assessed by the experimental leaf packs, was associated with shredder biomass, but not with shredder abundance. This result suggests that macroinvertebrates are important for leaf detritus processing and that their biomass reflects their activity, presumably because it is related to their secondary production and perhaps non-consumptive action. Their activity was observed at the scale of leaf packs and not at the scale of variation in canopy cover because apparently canopy did not modulate availability of leaves, which were apparently not limiting to the shredders

Seasonal and spatial differences in feeding habits of the Neotropical otter Lontra longicaudis (Carnivora: Mustelidae) in a coastal catchment of southeastern Brazil

The diet of the Neotropical otter Lontra longicaudis (Olfers, 1818) is one of the best known aspects of its biology throughout its distribution range. However, most dietary studies have been undertaken during short time periods, making it difficult to identify temporal patterns in the feeding behavior of the species. The present study aimed to describe the diet of L. longicaudis in the lower region of the Mambucaba Catchment, state of Rio de Janeiro, Brazil, during a three year period, based on analyses of spraints (feces). The results show fish as the main prey item (frequency of occurrence, FO = 85.78%), as already described in previous studies. Crustaceans were the second main prey (FO = 70.67%), occurring in the spraints during the whole year, however presenting a higher frequency of occurrence than fish in samples collected during some months. Anurans were the third most important prey item (FO = 9.56%) and mammals, birds and reptiles were preyed upon only rarely (less than 4%). Fish and crustaceans were present in the diet of the species throughout the year and frogs were important mostly from June to August (dry season). This higher rate of predation on amphibians during the drier months was probably related to the decrease of the main prey

Heterogeneity and scaling of photosynthesis, respiration, and nitrogen uptake in three Atlantic Rainforest streams

Leaves, epilithon, macrophytes, and fine benthic organic material are central ecosystem compartments to food webs and mediate nutrient fluxes in streams. Most estimates of gross primary production (GPP) and ecosystem respiration (ER) are made at a reach scale, averaging across compartments. Thus, there is little information on how individual compartments contribute to and scale up to whole-stream estimates across watersheds. We compared estimates of GPP, ER, and nitrogen (N) uptake of individual ecosystem compartments (dm) and stream reaches (similar to 100 m) in three sizes of streams in a preserved Atlantic Rainforest watershed. The smallest stream had dense forest canopy cover, whereas the largest was more open. We measured substratum-specific rates of GPP and ER, as well as ammonium and nitrate N-15 uptake in recirculating chambers. We compared these decimeter-scale measurements to whole-stream estimates, using single-station dissolved oxygen (GPP and ER) and pulsed N uptake methods. Epilithon and macrophytes (when present) were the dominant GPP and N uptake compartments in open-canopy sites, and leaves contributed strongly to ER at all sites, even though they covered <3 percent of the stream bottom. Ammonium and nitrate uptake per unit N content varied significantly among substrata and streams. Upscaled inorganic N uptake per unit area was greater when macrophytes were present. Chamber measurements overestimated metabolic rates in the larger streams, but not in the smallest one. The smallest transient storage zone streams were more active than the biggest one, and this influenced the mismatch between whole-stream and chamber nutrient uptake estimates. We conclude that scaling to the whole watershed requires information on location in the watershed (e.g., where canopy cover is dense), rates of individual compartments, and reach-specific hydrodynamic information as influenced by large-scale geomorphic details (i.e., the size and activity of the transient storage zones)