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

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world\u27s 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\u27s microbial diversity

Summer Marine Bacterial Community Composition of the Western Antarctic Peninsula

The Western Antarctic Peninsula has experienced dramatic warming due to climate change over the last 50 years and the consequences to the marine microbial community are not fully clear. The marine bacterial community are fundamental contributors to biogeochemical cycling of nutrients and minerals in the ocean. Molecular data of bacteria from the surface waters of the Western Antarctic Peninsula are lacking and most existing studies do not capture the annual variation of bacterial community dynamics. In this study, 15 different 16S rRNA gene amplicon samples covering 3 austral summers were processed and analyzed to investigate the marine bacterial community composition and its changes over the summer season. Between the 3 summer seasons, a similar pattern of dominance in relative community composition by the classes of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes was observed. Alphaproteobacteria were mainly composed of the order Rhodobacterales and increased in relative abundance as the summer progressed. Gammaproteobacteria were represented by a wide array of taxa at the order level. The class Bacteroidetes had the highest relative abundance in the early summer and decreased as the season progressed. Bacteroidetes were primarily represented by the order Flavobacteriales and genus Polaribacter. A high degree of interannual variability was observed for some taxa, like the order Sphingobacteriales, which exhibited a high relative abundance in only 1 season. Richness and evenness diversity measures were found to be at the lowest during phytoplankton blooms, and these diversity measures were observed to increase by the end of the summer. Code written for data processing and analysis are available at: https://github.com/codey-phoun/palmer_station_16

Phylogenetics and association analyses illustrate substantial cryptic diversity of a newly isolated collection of Cenococcum geophilum

The ectomycorrhizal fungus Cenococcum geophilum is distributed worldwide across multiple climates and soil types and is known to positively associate with a multitude of plant genera, possibly contributing to plant ability to tolerate inorganic contaminants in a soil environment. New C. geophilum isolates are easily cultured from soils in a laboratory setting, making this an ideal candidate for a model species with which to study multiple plant-fungal effects across a collection of novel isolates. However, C. geophilum is also genetically complex and, at 178Mbp, features one of the largest fungal genomes, necessitating the use of the novel restriction-associated DNA sequencing (RADseq) technique which produces robust de novo single nucleotide polymorphism (SNP) detection. A preliminary investigation into the phylogenetic relationship of \u3e200 new C. geophilum isolates from the United States Pacific Northwest (PNW) region using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) strongly resolved (\u3e80%) 15 cryptic clades. An investigation of the worldwide C. geophilum collection using GAPDH resolved \u3e30 cryptic clades. In both collections, at least two cryptic clades incorporated extreme spatial diversity in the form of cross-regional, cross-country, and international strains. Phylogenetic analyses of 171 PNW isolates conducted using RADseq strongly supported (\u3e80%) the 15 PNW clades using the de novo dataset assembly at a per-site depth of at least 10%. Direct comparison of the PNW ITS and GAPDH gene regions indicated strong evidence of sexual recombination and additional analyses confirmed high levels of incongruency between the two genes. However, when these same analyses were conducted on the RADseq de novo dataset, no strong evidence of recombination was detected across the PNW collection, suggesting this collection represents a hybridized clonal population with rare localized sexual recombination. An association analysis study linked heavy metal resistance of 56 C. geophilum isolates to significant associations detected from the de novo and reference-based RADseq assemblies, finding that the de novo assembly provided a more robust association dataset linked to a series of metabolic and ion-binding protein coding regions as well as two proteins which may be directly involved in resistance to cadmium within isolates from two PNW sites

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward