RESUMEN
BACKGROUND: Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. RESULTS: Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. CONCLUSIONS: For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology.
Asunto(s)
Biota , Ecología/métodos , Biología Computacional/métodosRESUMEN
Microbial communities play a major role in terrestrial ecosystem functioning, but the determinates of their diversity and functional interactions are not well known. In this study, we explored leaf litter fungal diversity in a diverse Panama lowland tropical forest in which a replicated factorial N, P, K and micronutrient fertilization experiment of 40 × 40 m plots had been ongoing for nine years. We extracted DNA from leaf litter samples and used fungal-specific amplification and a 454 pyrosequencing approach to sequence two loci, the nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear ribosomal large subunit (LSU) D1 region. Using a 95% sequence similarity threshold for ITS1 spacer recovered a total of 2523 OTUs, and the number of unique ITS1 OTUs per 0.5-1.0 g leaf litter sample ranged from 55 to 177. Ascomycota were the dominant phylum among the leaf litter fungi (71% of the OTUs), followed by Basidiomycota (26% of the OTUs). In contrast to our expectations based on temperate ecosystems, long-term addition of nutrients increased, rather than decreased, species richness relative to controls. Effect of individual nutrients was more subtle and seen primarily as changes in community compositions especially at lower taxonomic levels, rather than as significant changes in species richness. For example, plots receiving P tended to show a greater similarity in community composition compared to the other nutrient treatments, the +PK, +NK and +NPK plots appeared to be more dominated by the Nectriaceae than other treatments, and indicator species for particular nutrient combinations were identified.
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Biodiversidad , Fertilizantes/microbiología , Hongos/genética , Metagenoma/genética , Hojas de la Planta/microbiología , Microbiología del Suelo , Árboles , Secuencia de Bases , ADN Espaciador Ribosómico/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Datos de Secuencia Molecular , Nitrógeno , Panamá , Fósforo , Potasio , Homología de Secuencia , Clima TropicalRESUMEN
Taxa with smaller individuals tend to have shorter generation times and higher local abundance and diversity. The scaled specialization hypothesis (SSH) posits that taxocenes of smaller individuals should differentiate more rapidly and thoroughly along physiochemical gradients of a given age and extent. In a Panama rainforest, we evaluated how bacteria, fungi, and ants responded to two such gradients: one topographic and the other arising from nine years of NPK fertilization. Terminal restriction fragment length polymorphism (T-RFLP) delineated bacteria and fungi operational taxonomic units (OTUs); traditional taxonomy delineated the ants. Bacteria had higher local species richness than fungi and ants (averaging 48 vs. 30 vs. 6 OTUs in < 0.25 m2). Bacteria OTUs were also more widely distributed (17% of OTUs were found on > or = 50% of sample plots compared to 3% for fungi and ants). Consistent with SSH, bacterial composition differed across short-term (+N and +P) and long-term (topographic) gradients; fungal taxocenes differed only along the long-term gradient; and ant taxocenes were homogenous across both. Body size can help predict community responses to a changing environment.
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Hormigas/clasificación , Bacterias/clasificación , Hongos/clasificación , Árboles , Clima Tropical , Animales , Hormigas/fisiología , Biodiversidad , DemografíaRESUMEN
Suillus quiescens sp. nov. is common under Pinus muricata on Santa Cruz and Santa Rosa Islands in the northern Channel Islands of California, and we subsequently found it fruiting at Point Reyes National Seashore on the central coast of California. Sequences from the internal transcribed spacer region show that it is distinct from all 44 species of Suillus tested, and features of its morphology separate it from all other unsequenced species. Suillus quiescens has a broader distribution than coastal California because it also was encountered as ectomycorrhizae on roots of pine seedlings from the eastern Sierra Nevada, coastal Oregon and the southern Cascade Mountains. The reason it had not been identified from these areas might be due to its resemblance to S. brevipes at maturity or it might be a rare fruiter that persists in the spore bank.
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Basidiomycota/aislamiento & purificación , Pinus , Enfermedades de las Plantas/microbiología , Secuencia de Bases , Basidiomycota/genética , Basidiomycota/ultraestructura , California , ADN de Hongos/química , ADN de Hongos/genética , ADN Espaciador Ribosómico/química , ADN Espaciador Ribosómico/genética , Geografía , Datos de Secuencia Molecular , Oregon , Filogenia , Reacción en Cadena de la Polimerasa , Alineación de Secuencia , Análisis de Secuencia de ADNRESUMEN
Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete that has evolved from heterothallic ancestors. Throughout its life cycle, it is predominantly heterokaryotic for mating type, and thereby self-fertile. However, studies of N. tetrasperma have revealed the occasional production of self-sterile asexual and sexual spores of a single-mating type, indicating that it can be functionally heterothallic. Here, we report the extensive sampling and isolation of natural, heterokaryotic, strains of N. tetrasperma from the United Kingdom (UK): 99 strains were collected from Surrey, England, and four from Edinburgh, Scotland. We verified by phylogenetic analyses that these strains belong to N. tetrasperma. We isolated cultures from single germinated asexual spores (conidia) from 17 of these newly sampled UK strains from Surrey, and 16 previously sampled strains of N. tetrasperma from New Zealand (NZ). Our results show that the N. tetrasperma strains from the UK population produced a significantly greater proportion of self-sterile, homokaryotic conidia than the NZ population: the proportion of homokaryotic conidia was 42.6 % (133/312 spores) and 15.3 % (59/386) from the UK and the NZ populations, respectively. Although homokaryons recovered from several strains show a bias for one of the mating types, the total ratio of mat A to mat a mating type in homokaryons (UK: 72/61, NZ 28/31) did not deviate significantly from the expected 1:1 ratio for either of these populations. These results indicate that different populations exhibit differences in their life cycle characteristics, and that a higher degree of outcrossing might be expected from the UK population. This study points to the importance of studying multiple strains and populations when investigating life history traits of an organism with a complex life cycle, as previously undetected differences between populations may be revealed.