Anatomia ecológica do lenho de espécies arbustivas e arbóreas que ocorrem naturalmente em bosques com drástico gradiente de precipitação ao Noroeste da Patagônia, Argentina

A utilização de gradientes ambientais no estudo de comunidades vegetais possibilita a eleição de sítios onde há a predominância de um fator abiótico que determina o sucesso ou o fracasso de espécies ao longo de sua extensão. Entre as inúmeras ferramentas utilizadas no estudo de gradientes climáticos, se destaca a anatomia do lenho, pois, é um ramo da ciência que permite analisar, além dos aspectos espaciais, os aspectos temporais dos sítios por meio dos anéis de crescimento. Além disso, a ampla distribuição das plantas lenhosas ao longo do globo possibilita análises em praticamente todos os tipos de biomas e ecossistemas terrestres. Dentro desse contexto estão os bosques andino-patagônicos de Araucaria araucana (Pehuén) ao norte de sua distribuição na Argentina. Esses bosques ocupam territórios caracterizados por um acentuado gradiente de precipitação, que vai de cerca de 3000 a 100 milímetros anuais, entre a cordilheira do Andes e a estepe patagônica, que os define como bosques mésicos e xéricos, com diferenças ecológicas que condicionam a formação vegetal, dinâmica, estrutura, relações com o clima e vulnerabilidade em cenários de mudanças ambientais. O objetivo do projeto foi descrever e analisar comparativamente a estrutura anatômica do lenho de 33 espécies arbóreas e arbustivas ocorrentes ao longo de um gradiente de precipitação, entre a encosta da cordilheira dos Andes e a estepe Patagônica, para verificar possíveis alterações anatômicas que permitam a determinação de tendências e elucidem os limites de distribuição das espécies. Foram coletadas amostras não destrutivas de lenho durante três expedições para a Patagônia entre 2012 e 2014, seguidas de procedimentos laboratoriais de confeccção de lâminas histológicas, preparo de amostras para análises dendrocronológicas, captura de imagens com câmeras acopladas a microscópios óptico e eletrônico de varredura, mensurações, descrições e análises comparativas com o auxílio de softwares. Foram identificados caracteres anatômicos exclusivos de sítios secos e úmidos que permitiram a caracterização, posicionamento ao longo do gradiente de precipitação e grupamento de espécies xerófitas e mesófitas; A ultra-estrutura das pontoações de traqueídeos de Araucaria araucana apresentou diferenças marcantes na frequência e porosidade de suas membranas, sendo maior e menos porosas em sítios xéricos, e menor e mais porosas nos mésicos; a chave dicotômica microscópica permitiu a identificação das 32 espécies arbustivas, as espécies Chuquiraga oppositifolia e Nothofagus antarctica apresentaram potencial dendrocronológico, e foram identificadas tendências anatômicas latitudinais influenciadas pelo clima nos extremos da América do Sul. A anatomia do lenho se mostrou uma ferramenta confiável no estudo de um gradiente de precipitação na Patagônia argentina, e os resultados apontam para riscos de embolismos e morte induzida por falha no sistema hidráulico de Araucaria araucana ao longo de todo o gradiente, em função do atual cenário climático, e suas projeções em médio e longo prazos.

Fatores abióticos condicionantes da distribuição de espécies arbóreas em quatro formações florestais do Estado de São Paulo

No estudo das comunidades florestais, estabelecer a importância relativa dos fatores que definem a composição e a distribuição das espécies é um desafio. Em termos de gradientes ambientais o estudo das respostas das espécies arbóreas são essenciais para a compreensão dos processos ecológicos e decisões de conservação. Neste sentido, para contribuir com a elucidação dos processos ecológicos nas principais formações florestais do Estado de São Paulo (Floresta Ombrófila Densa de Terras Baixas, Floresta Ombrófila Densa Submontana, Floresta Estacional Semidecidual e Savana Florestada) este trabalho objetivou responder as seguintes questões: (I) a composição florística e a abundância das espécies arbóreas, em cada unidade fitogeográfica, variam conforme o gradiente edáfico e topográfico?; (II) características do solo e topografia podem influenciar na previsibilidade de ocorrência de espécies arbóreas de ampla distribuição em diferentes tipos vegetacionais? (III) existe relação entre o padrão de distribuição espacial de espécies arbóreas e os parâmetros do solo e topografia? O trabalho foi realizado em parcelas alocadas em unidades de conservação (UC) que apresentaram trechos representativos, em termos de conservação e tamanho, das quatro principais formações florestais presentes no Estado de São Paulo. Em cada UC foram contabilizados os indivíduos arbóreos (CAP ≥ 15 cm), topografia, dados de textura e atributos químicos dos solos em uma parcela de 10,24 ha, subdividida em 256 subparcelas. Análises de correspodência canônica foram aplicadas para estabelecer a correspondência entre a abundância das espécies e o gradiente ambiental (solo e topografia). O método TWINSPAN modificado foi aplicado ao diagrama de ordenação da CCA para avaliar a influência das variáveis ambientais (solo e topografia) na composição de espécies. Árvores de regressão \"ampliadas\" (BRT) foram ajustadas para a predição da ocorrência das espécies segundo as variáveis de solo e topografia. O índice de Getis-Ord (G) foi utilizado para determinar a autocorrelação espacial das variáveis ambientais utilizadas nos modelos de predição da ocorrência das espécies. Nas unidades fitogeográficas analisadas, a correspondência entre o gradiente ambiental (solo e topografia) e a abundância das espécies foi significativa, especialmente na Savana Florestada onde observou-se a maior relação. O solo e a topografia também se relacionaram com a semelhança na composição florística das subparcelas, com exceção da Floresta Estacional Semicidual (EEC). As principais variáveis de solo e topografia relacionadas a flora em cada UC foram: (1) Na Floresta Ombrófila Densa de Terras Baixas (PEIC) - teor de alumínio na camada profunda (Al (80-100 cm)) que pode refletir os teor de Al na superfície, acidez do solo (pH(H2O) (5-25 cm)) e altitude, que delimitou as áreas alagadas; (2) Na Floresta Ombrófila Densa Submontana (PECB) - altitude, fator que, devido ao relevo acidentado, influencia a temperatura e incidência de sol no sub-bosque; (3) Na Savana Florestada (EEA) - fertilidade, tolerância ao alumínio e acidez do solo. Nos modelos de predição BRT, as variáveis químicas dos solos foram mais importantes do que a textura, devido à pequena variação deste atributo no solo nas áreas amostradas. Dentre as variáveis químicas dos solos, a capacidade de troca catiônica foi utilizada para prever a ocorrência das espécies nas quatro formações florestais, sendo particularmente importante na camada mais profunda do solo da Floresta Ombrófila Densa de Terras Baixas (PEIC). Quanto à topografia, a altitude foi inserida na maioria dos modelos e apresentou diferentes influências sobre as áreas de estudo. De modo geral, para presença das espécies de ampla distribuição observou-se uma mesma tendência quando à associação com os atributos dos solos, porém com amplitudes dos descritores edáficos que variaram de acordo com a área de estudo. A ocorrência de Guapira opposita e Syagrus romanzoffiana, cujo padrão variou conforme a escala, foi explicada por variáveis com padrões espaciais agregados que somaram entre 30% e 50% de importância relativa no modelo BRT. A presença de A. anthelmia, cujo padrão também apresentou certo nível de agregação, foi associada apenas a uma variável com padrão agregado, a altitude (21%), que pode ter exercido grande influência na distribuição da espécie ao delimitar áreas alagadas. T. guianensis se associou a variáveis ambientais preditoras com padrão espacial agregado que somaram cerca de 70% de importância relativa, o que deve ter sido suficiente para estabelecer o padrão agregado em todas as escalas. No entanto, a influência dos fatores ambientais no padrão de distribuição da espécie não depende apenas do ótimo ambiental da espécie, mas um resultado da interação espécie-ambiente. Concluiu-se que: (I) características edáficas e topográficas explicaram uma pequena parcela da composição florística, em cada unidade fitogeográfica, embora a ocorrência de algumas espécies tenha se associado ao gradiente edáfico e topográfico; (II) a partir de características dos solos e da topografia foi possível prever a presença de espécies arbóreas, que apresentaram particularidades em relação a sua associação com o solo de cada fitofisionomia; (III) a partir de associações descritivas o solo e a topografia influenciam o padrão de distribuição espacial das espécies, na proporção em que contribuem para a presença das mesmas.

Plant competition; an analysis of community functions,

Bibliography: p. 335-340.

CITES, Appendices I, II and III to the Convention on International Trade in Endangered Species of Wild Fauna and Flora.

"June 1997"--P. [4] of cover.

Caring for our natural community : region 1 - threatened, endangered & sensitive species program /

Shipping list no.: 89-191-P.

Local impacts of global change: shifting range limits, advancing phenology, and communicating research

Thesis (Ph.D.)--University of Washington, 2016-06

Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity

The diversity of the culturable microbial communities was examined in two sponge species-Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga-Flavobacterium-Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.

Testing the niche apportionment hypothesis with parasite communities: is random assortment always the rule?

Niche apportionment models have only been applied once to parasite communities. Only the random assortment model (RA), which indicates that species abundances are independent from each other and that interspecific competition is unimportant, provided a good fit to 3 out of 6 parasite communities investigated. The generality of this result needs to be validated, however. In this study we apply 5 niche apportionment models to the parasite communities of 14 fish species from the Great Barrier Reef. We determined which model fitted the data when using either numerical abundance or biomass as an estimate of parasite abundance, and whether the fit of niche apportionment models depends on how the parasite community is defined (e.g. ecto, endoparasites or all parasites considered together). The RA model provided a good fit for the whole community of parasites in 7 fish species when using biovolume (as a surrogate of biomass) as a measure of species abundance. The RA model also fitted observed data when ecto- and endoparasites were considered separately, using abundance or biovolume, but less frequently. Variation in fish sizes among species was not associated with the probability of a model fitting the data. Total numerical abundance and biovolume of parasites were not related across host species, suggesting that they capture different aspects of abundance. Biovolume is not only a better measurement to use with niche-orientated models, it should also be the preferred descriptor to analyse parasite community structure in other contexts. Most of the biological assumptions behind the RA model, i.e. randomness in apportioning niche space, lack of interspecific competition, independence of abundance among different species, and species with variable niches in changeable environments, are in accordance with some previous findings on parasite communities. Thus, parasite communities may generally be unsaturated with species, with empty niches, and interspecific interactions may generally be unimportant in determining parasite community structure.

A multi-faceted diagnostic approach to lung infections in patients with cystic fibrosis

One in 3,000 people in the US are born with cystic fibrosis (CF), a genetic disorder affecting the reproductive system, pancreas, and lungs. Lung disease caused by chronic bacterial and fungal infections is the leading cause of morbidity and mortality in CF. Identities of the microbes are traditionally determined by culturing followed by phenotypic and biochemical assays. It was first thought that the bacterial infections were caused by a select handful of bacteria such as S. aureus, H. influenzae, B. cenocepacia, and P. aeruginosa. With the advent of PCR and molecular techniques, the polymicrobial nature of the CF lung became evident. The CF lung contains numerous bacteria and the communities are diverse and unique to each patient. The total complexity of the bacterial infections is still being determined. In addition, only a few members of the fungal communities have been identified. Much of the fungal community composition is still a mystery. This dissertation addresses this gap in knowledge. A snap shot of CF sputa bacterial community was obtained using the length heterogeneity-PCR community profiling technique. The profiles show that south Florida CF patients have a unique, diverse, and dynamic bacterial community which changes over time. The identities of the bacteria and fungi present were determined using the state-of-the-art 454 sequencing. Sequencing results show that the CF lung microbiome contains commonly cultured pathogenic bacteria, organisms considered a part of the healthy core biome, and novel organisms. Understanding the dynamic changes of these identified microbes will ultimately lead to better therapeutical interventions. Early detection is key in reducing the lung damage caused by chronic infections. Thus, there is a need for accurate and sensitive diagnostic tests. This issue was addressed by designing a bacterial diagnostic tool targeted towards CF pathogens using SPR. By identifying the organisms associated with the CF lung and understanding their community interactions, patients can receive better treatment and live longer.

Antimicrobial effect of Artemisia species on Pseudomonas aeruginosa

Antibiotic resistance has emerged as a severe problem in hospital-acquired infectious disease. The Gram-negative bacterium Pseudomonas aeruginosa is found to cause secondary infection in immune-compromised patients. Unfortunately, it is resistant to virtually all β-lactam antibiotics such as penicillin, cephalosporin and others. Researchers are seeking for new compounds to treat several antibiotic-resistant bacterial strains. Artemisia plant extracts are commonly used for their therapeutic properties by natives throughout dry regions of North and South America. Here, they are administered as an alternative medicine for stomach problems and other complex health issues. In this study, the antimicrobial effects of plant extracts from several Artemisia species as well as compounds dehydroleucodine and dehydroparishin-B (sesquiterpenes derived specifically from A. douglasiana) were used as treatments against the pathogenicity effects of P. aeruginosa. Results showed that both compounds effectively inhibit the secretion of LasB elastase, biofilm formation and type III secretion, but fail to control LasA protease. This is a significant observation because these virulent factors are crucial in establishing P.aeruginosa infection. The results from this study signify a plausible role for future alternative therapy in the biomedical field, which recommends DhL and DhP can be studied as key compounds against bacterial infections of Pseudomonas aeruginosa.

An Analytical Workflow for Metagenomic Data and its Application to the Study of Chronic Obstructive Pulmonary Disease (COPD)

Metagenomics is the culture-independent study of genetic material obtained directly from environmental samples. It has become a realistic approach to understanding microbial communities thanks to advances in high-throughput DNA sequencing technologies over the past decade. Current research has shown that different sites of the human body house varied bacterial communities. There is a strong correlation between an individual’s microbial community profile at a given site and disease. Metagenomics is being applied more often as a means of comparing microbial profiles in biomedical studies. The analysis of the data collected using metagenomics can be quite challenging and there exist a plethora of tools for interpreting the results. An automatic analytical workflow for metagenomic analyses has been implemented and tested using synthetic datasets of varying quality. It is able to accurately classify bacteria by taxa and correctly estimate the richness and diversity of each set. The workflow was then applied to the study of the airways microbiome in Chronic Obstructive Pulmonary Disease (COPD). COPD is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals and COPD patients. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers and sequenced by 454 pyrosequencing. A total of 56 individuals were recruited for the study. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified. These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.

A Multi-Faceted Diagnostic Approach to Lung Infections in Patients with Cystic Fibrosis

One in 3,000 people in the US are born with cystic fibrosis (CF), a genetic disorder affecting the reproductive system, pancreas, and lungs. Lung disease caused by chronic bacterial and fungal infections is the leading cause of morbidity and mortality in CF. Identities of the microbes are traditionally determined by culturing followed by phenotypic and biochemical assays. It was first thought that the bacterial infections were caused by a select handful of bacteria such as S. aureus, H. influenzae, B. cenocepacia, and P. aeruginosa. With the advent of PCR and molecular techniques, the polymicrobial nature of the CF lung became evident. The CF lung contains numerous bacteria and the communities are diverse and unique to each patient. The total complexity of the bacterial infections is still being determined. In addition, only a few members of the fungal communities have been identified. Much of the fungal community composition is still a mystery. This dissertation addresses this gap in knowledge. A snap shot of CF sputa bacterial community was obtained using the length heterogeneity-PCR community profiling technique. The profiles show that south Florida CF patients have a unique, diverse, and dynamic bacterial community which changes over time. The identities of the bacteria and fungi present were determined using the state-of-the-art 454 sequencing. Sequencing results show that the CF lung microbiome contains commonly cultured pathogenic bacteria, organisms considered a part of the healthy core biome, and novel organisms. Understanding the dynamic changes of these identified microbes will ultimately lead to better therapeutical interventions. Early detection is key in reducing the lung damage caused by chronic infections. Thus, there is a need for accurate and sensitive diagnostic tests. This issue was addressed by designing a bacterial diagnostic tool targeted towards CF pathogens using SPR. By identifying the organisms associated with the CF lung and understanding their community interactions, patients can receive better treatment and live longer.

Quantitative Comparison of Plant Community Hydrology Using Large-Extent, Long-Term Data

Large-extent vegetation datasets that co-occur with long-term hydrology data provide new ways to develop biologically meaningful hydrologic variables and to determine plant community responses to hydrology. We analyzed the suitability of different hydrological variables to predict vegetation in two water conservation areas (WCAs) in the Florida Everglades, USA, and developed metrics to define realized hydrologic optima and tolerances. Using vegetation data spatially co-located with long-term hydrological records, we evaluated seven variables describing water depth, hydroperiod length, and number of wet/dry events; each variable was tested for 2-, 4- and 10-year intervals for Julian annual averages and environmentally-defined hydrologic intervals. Maximum length and maximum water depth during the wet period calculated for environmentally-defined hydrologic intervals over a 4-year period were the best predictors of vegetation type. Proportional abundance of vegetation types along hydrological gradients indicated that communities had different realized optima and tolerances across WCAs. Although in both WCAs, the trees/shrubs class was on the drier/shallower end of hydrological gradients, while slough communities occupied the wetter/deeper end, the distribution ofCladium, Typha, wet prairie and Salix communities, which were intermediate for most hydrological variables, varied in proportional abundance along hydrologic gradients between WCAs, indicating that realized optima and tolerances are context-dependent.

Diatom abundance in surface sediments of the Southern Ocean

Based on the quantitative analysis of diatom assemblages preserved in 274 surface sediment samples recovered in the Pacific, Atlantic and western Indian sectors of the Southern Ocean we have defined a new reference database for quantitative estimation of late-middle Pleistocene Antarctic sea ice fields using the transfer function technique. The Detrended Canonical Analysis (DCA) of the diatom data set points to a unimodal distribution of the diatom assemblages. Canonical Correspondence Analysis (CCA) indicates that winter sea ice (WSI) but also summer sea surface temperature (SSST) represent the most prominent environmental variables that control the spatial species distribution. To test the applicability of transfer functions for sea ice reconstruction in terms of concentration and occurrence probability we applied four different methods, the Imbrie and Kipp Method (IKM), the Modern Analog Technique (MAT), Weighted Averaging (WA), and Weighted Averaging Partial Least Squares (WAPLS), using logarithm-transformed diatom data and satellite-derived (1981-2010) sea ice data as a reference. The best performance for IKM results was obtained using a subset of 172 samples with 28 diatom taxa/taxa groups, quadratic regression and a three-factor model (IKM-D172/28/3q) resulting in root mean square errors of prediction (RMSEP) of 7.27% and 11.4% for WSI and summer sea ice (SSI) concentration, respectively. MAT estimates were calculated with different numbers of analogs (4, 6) using a 274-sample/28-taxa reference data set (MAT-D274/28/4an, -6an) resulting in RMSEP's ranging from 5.52% (4an) to 5.91% (6an) for WSI as well as 8.93% (4an) to 9.05% (6an) for SSI. WA and WAPLS performed less well with the D274 data set, compared to MAT, achieving WSI concentration RMSEP's of 9.91% with WA and 11.29% with WAPLS, recommending the use of IKM and MAT. The application of IKM and MAT to surface sediment data revealed strong relations to the satellite-derived winter and summer sea ice field. Sea ice reconstructions performed on an Atlantic- and a Pacific Southern Ocean sediment core, both documenting sea ice variability over the past 150,000 years (MIS 1 - MIS 6), resulted in similar glacial/interglacial trends of IKM and MAT-based sea-ice estimates. On the average, however, IKM estimates display smaller WSI and slightly higher SSI concentration and probability at lower variability in comparison with MAT. This pattern is a result of different estimation techniques with integration of WSI and SSI signals in one single factor assemblage by applying IKM and selecting specific single samples, thus keeping close to the original diatom database and included variability, by MAT. In contrast to the estimation of WSI, reconstructions of past SSI variability remains weaker. Combined with diatom-based estimates, the abundance and flux pattern of biogenic opal represents an additional indication for the WSI and SSI extent.

Benthic foraminifera in surface sediments, South Atlantic

Sixty surface sediment samples from the eastern South Atlantic Ocean including the Walvis Ridge, the Angola and Cape basins, and the Southwest African continental margin were analysed for their benthic foraminiferal content to unravel faunal distribution patterns and ecological preferences. Live (stained with Rose Bengal) and dead faunas were counted separately and then each grouped by Q-mode principal component analysis into seven principal faunal end-members. Then, multiple regression technique was used to correlate Recent assemblages with available environmental variables and to finally differentiate between four principal groups of environmental agents acting upon the generation of benthic foraminiferal assemblages: (1) seasonality of food supply and organic carbon flux rates, together with oxygen content in the pore and bottom waters; (2) lateral advection of deep-water masses; (3) bottom water carbonate corrosiveness; and (4) energetic state at the benthic boundary layer and grain size composition of the substrate. Food supply and corresponding dissolved oxygen contents in the pore and bottom waters turned out to be the most important factors which control the distribution pattern of the Recent benthic foraminifera. At the continental margin, in the zone of coastal upwelling and its mixing area, benthic foraminiferal assemblages are dominated by stenobathic high-productivity faunas, characterized by elevated standing stocks, low diversities and a large number of endobenthic living species. At the continental shelf and upper continental slope the live assemblages are characterized by Rectuvigerina cylindrica, Uvigerina peregrina s.1., Uvigerina auberiana and Rhizammina spp. while the dead assemblages are characterized by Cassidulina laevigata, Bolivina dilatata, Bulimina costata and B. mexicana. At the lower continental slope strong influence of high organic matter fluxes on the species composition is restricted to the area off the Cunene river mouth, where the live assemblage is dominated by Uvigerina peregrina s.1., the corresponding dead assemblage by Melonis barleeanum and M. zaandamae. In the adjacent areas of the lower continental slope the biocoenosis is characterized by Reophax bilocularis, and Epistominella exigua which becomes dominant in the corresponding dead assemblage. At the Walvis Ridge and in the abyssal Angola and Cape basins, where organic matter fluxes are low and highly seasonal, benthic foraminiferal assemblages reflect both the oligotrophic situation and the deep and bottom water mass configuration. The top and flanks of the Walvis Ridge are inhabited by the Rhizammina, Psammosphaera and R. bilocularis live assemblages, the corresponding dead assemblages are dominated by G. subglobosa on the ridge top and E. exigua on the flanks. Within the highly diverse E. exigua dead assemblage several associated epibenthic species coincide with the core of NADW between about 1600 and 3700 m water depth. These species include Osangularia culter, Cibicidoides kullenbergi, Melonis pompilioides, Bolivinita pseudothalmanni and Bulimina alazanensis. The assemblages of the abyssal Cape and Angola basins are characterized by Nuttallides umbonifer and a high proportion of agglutinated species. These species are adapted to very low organic matter fluxes and a carbonate corrosive environment.