A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

Pleistocene range expansions might explain striking disjunctions between eastern Brazil, Andes and Mesoamerica in leandra s.str. (melastomataceae)

Leandra s.str. clade has around 200 species nearly restricted to eastern Brazil. Most species in this group are narrow endemics, but a few present striking disjunct distributions between eastern Brazil and Andes or Mesoamerica. Given the predominantly “montane” distribution observed in most Leandra s.str., we hypothesized that cyclical range expansions during colder Pleistocene periods, followed by local extinctions during warmer interglacial periods, could have shaped the distribution of the disjunct species in this clade. In order to gather support for this biogeographical scenario in a phylogenetic framework, the species that occur outside eastern Brazil were identified, ages of the dispersal events estimated, climatic niche models for the disjuncts were generated, and the climatic envelope of these species compared. Our results place all dispersal events from eastern Brazil to Andes or Mesoamerica during the Pleistocene. Climatic niche modeling indicates a potential range expansion during the Pleistocene colder times for the disjunct species. Although the surpassing of the “dry diagonal” could have been facilitated during glacial periods, this open corridor is an effective barrier for Leandra, given the reduced number of species that dispersed beyond an eastern Brazilian origin. Additionally, the disjunct species do not present significant differences in their climatic envelopes to the non-disjunct species. Our results provide support to a short-dispersion/stepping-stone migration scenario to account for the observed disjunctions in this clade. Range expansions during Pleistocene colder periods followed by local extinctions during interglacial periods could have shaped the distribution of Leandra s.str57664665

Phylogenetics, morphology and circumscription of Cambessedesieae: a new Neotropical tribe of Melastomataceae

Systematic studies based on DNA sequences have shown that some traditional tribal delimitations in Melastomataceae remain unresolved, such as the 'Merianthera and allies' clade, an informal group which has not been formally assigned to a tribe. This clade includes Behuria, Cambessedesia, Dolichoura, Huberia and Merianthera and occurs mainly at high elevations in the Atlantic Forest and cerrado biomes of Brazil. Behuria, Dolichoura, Huberia and Merianthera were tradionally placed in Merianieae based on overall similar morphology. The assignment of Cambessedesia to Microlicieae has been challenged and its tribal placement needs re-evaluation. To infer the monophyly of the genera and revise generic limits we analysed DNA markers of three plastid (atpF-atpH, psbK-psbL and trnS-trnG), two ribosomal (nrETS and nrITS) and a segment of a low-copy nuclear gene (waxy), using maximum likelihood and Bayesian inference. We also selected 12 morphological characters to reconstruct an ancestral character estimation analysis. Our results recovered Cambessedesia and Merianthera as monophyletic lineages together with monophyletic Huberia and Dolichoura nested in a paraphyletic Behuria. We propose and describe for the first time the tribe Cambessedesieae based on molecular, morphological and geographical data. As recognized here, Cambessedesieae consist of Cambessedesia, Merianthera and an expanded Huberia (including Behuria and Dolichoura)1903281302sem informaçã

The first complete plastid genomes of Melastomataceae are highly structurally conserved

Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies

Contrasting patterns of taxonomic, phylogenetic and functional variation along a Costa Rican altitudinal gradient in the plant family Melastomataceae

The functional composition of plant communities in montane regions has been studied for decades, and most recent analyses find that environmentally favourable landscapes at lower altitudes tend to be dominated by species with resource-acquisitive traits, while more resource-conservative taxa dominate higher-altitude communities. However, it is unclear the extent to which this pattern is driven by co-gradient variation within clades or changes in clade representation across the gradient. To test for co-gradient variation, species composition, phylogenetic structure and functional traits were quantified for 97 species within the plant family Melastomataceae at five locations across a 2500- m altitudinal gradient along Volcán Barva in Costa Rica. Average melastome leaf force to punch, specific leaf area and leaf size vary with altitude, while four other functional traits do not. Taxonomic dissimilarity between communities was correlated with altitudinal difference, while phylogenetic dissimilarity was correlated with altitudinal dissimilarity only when measured with a metric that emphasizes shallow turnover of the tips of the phylogeny. These results highlight how species turnover may be more pronounced than functional or phylogenetic variation along altitudinal gradients. In addition, these results highlight the conservation value of lowland tropical forests, which here harbour a disproportionate amount of phylogenetic and functional diversityLa composición funcional de las comunidades de plantas en las regiones montañosas se ha estudiado durante décadas, y los análisis más recientes encuentran que los paisajes ambientalmente favorables en altitudes más bajas tienden a estar dominados por especies con características de adquisición de recursos, mientras que los taxones más conservadores de recursos dominan las comunidades de altitudes más altas. . Sin embargo, no está claro hasta qué punto este patrón es impulsado por la variación del cogradiente dentro de los clados o los cambios en la representación de los clados a lo largo del gradiente. Para evaluar la variación del cogradiente, se cuantificaron la composición de especies, la estructura filogenética y los rasgos funcionales de 97 especies dentro de la familia de plantas Melastomataceae en cinco lugares a lo largo de un gradiente altitudinal de 2500 m a lo largo del Volcán Barva en Costa Rica. La fuerza promedio de la hoja de melastoma para perforar, el área foliar específica y el tamaño de la hoja varían con la altitud, mientras que otros cuatro rasgos funcionales no lo hacen. La disimilitud taxonómica entre comunidades se correlacionó con la diferencia altitudinal, mientras que la disimilitud filogenética se correlacionó con la disimilitud altitudinal solo cuando se midió con una métrica que enfatiza la rotación superficial de las puntas de la filogenia. Estos resultados resaltan cómo el recambio de especies puede ser más pronunciado que la variación funcional o filogenética a lo largo de los gradientes altitudinales. Además, estos resultados resaltan el valor de conservación de los bosques tropicales de tierras bajas, que aquí albergan una cantidad desproporcionada de diversidad filogenética y funcional.Universidad Nacional, Costa RicaEscuela de Ciencias Biológica

Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird▿ †

The hoatzin is unique among known avian species because of the fermentative function of its enlarged crop. A small-bodied flying foregut fermenter is a paradox, and this bird provides an interesting model to examine how diet selection and the gut microbiota contribute to maximizing digestive efficiency. Therefore, we characterized the bacterial population in the crop of six adult hoatzins captured from the wild. A total of 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% of the pooled species richness sampled, based on Good's coverage estimator, with CACE and Chao1 estimates of 1,709 and 1,795 species-level [99% identity] operational taxonomic units, respectively). Members of 9 of the ∼75 known phyla in Bacteria were identified in this gut habitat; the Firmicutes were dominant (67% of sequences, belonging to the classes Clostridia, Mollicutes, and Bacilli), followed by the Bacteroidetes (30%, mostly in the order Bacteroidales), Proteobacteria (1.8%), and Lentisphaerae, Verrucomicrobia, TM7, Spirochaetes, Actinobacteria, and Aminanaerobia (all <0.1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the “species” level and thus likely include novel cellulolytic lineages