Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

/pdf/diet-rapidly-and-reproducibly-alters-the-human-gut-drvn0pi8vp.pdf

Diet rapidly and reproducibly alters the human gut microbiome

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Microbes are the unseen majority in soil and comprise a large portion of lifes genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5‐20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

/pdf/the-unseen-majority-soil-microbes-as-drivers-of-plant-1yjo7xbywu.pdf

The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

UNITE (https://unite.ut.ee; Nilsson et al. 2018) is an international community of scientists and citizen scientists established in 2001. The ambition of UNITE is to develop: 1) datasets and tools for robust and reproducible molecular identification; 2) Persistent Identifiers based system for the communicating fungal species. Datasets of the nuclear ribosomal internal transcribed spacer (ITS) region, form the basis for UNITE. The current version includes nearly 1 million public fungal ITS sequences. Datasets are curated and annotated by community members. During the past 15 years, they made more than 275 000 improvements. In the complete absence of Latin names for species, UNITE offers a unique system where species hypotheses (SH) are provided with Digital Object Identifiers (DOIs). The current version 8 of UNITE offers more than 800 000 DOI-based SHs. One such SH DOI page is shown in Fig. 1. These DOI identifiers are also incorporated into the taxonomic backbone, making communication of taxa seamless in both directions. DOI identifiers of species hypotheses are also used by GBIF (Global Biodiversity Information Facility) in order to publish high-throughput sequencing taxon occurrence data in their data portal.
 UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources.
 Recent improvements include ITS-based species hypotheses for all eukaryotes and aggregation of full-length, high-quality ITS sequences generated by the PacBio Sequel system (https://www.pacb.com/products-and-services/sequel-system) from diverse material samples.

https://biss.pensoft.net/article/37402/download/pdf/

The UNITE Database for Molecular Identification and for Communicating Fungal Species

This paper presents Tomentella capitata and Tomentella brunneocystidia as new species based on molecular data and anatomical features. Both T. capitata and T. brunneocystidia form sister species with Tomentella pilosa. All three taxa are well supported by bootstrap values. Anatomically, T. capitata and T. brunneocystidia are very close and are similar in shape, size, ornamentation of basidiospores, and size and colour of subicular hyphae. Monomitic rhizomorphs sometimes covered by irregularly shaped thin hyphae are present in both species. Shape and pigmentation of the cystidia are the most discriminating features between T. capitata and T. brunneocystidia. The cystidia of T. capitata are maximum 35 μm long, show a distinctive globose apex and are sometimes covered with dark brown pigmentation and/or encrustation, whereas cystidia of T. brunneocystidia are bigger, up to 55 μm long, with a sub-capitate shape and dark blue to dark green contents all over their length. The differences to species, already described as having capitate and clavate cystidia, are discussed. A key for the identification of cystidioid Tomentella species is given.

Studies in African thelephoroid fungi: 1. Tomentella capitata and Tomentella brunneocystidia , two new species from Benin (West Africa) with capitate cystidia

Ectomycorrhizal fungal assemblages in tropical regions have remained relatively understudied compared to temperate ecosystems. Sea grape (Coccoloba uvifera) from the Polygonaceae family is a common ectomycorrhizal tree species inhabiting coastal habitats in neotropical forests. We sampled roots of C. uvifera in six locations around the Caribbean basin to characterize the associated ectomycorrhizal fungal assemblages at the regional scale. In accordance with earlier reports, sea grape ectomycorrhizal fungal communities were species-poor, implying ecological host specificity. Species of the /tomentella-thelephora lineage were the most species-rich group inhabiting roots of C. uvifera. Inclusive phylogenetic analyses of Thelephoraceae from Northeast, Central and South America indicated that the mycobionts of C. uvifera tend to cluster with taxa associated with North and Central American Pinus and Fagaceae rather than with South American taxa. This suggests that C. uvifera may have received multiple EcM symbionts from host switching events due to a common habitat in maritime sand dunes or more widely shared historical habitat in North America and the Caribbean Islands. Considering the absence of shared fungal taxa with other Coccoloba species from inland rain forest habitats, we hypothesize that distinct ectomycorrhizal associations of sea grape are primarily driven by stressful environmental conditions in maritime sand dunes.

Biogeography and Specificity of Ectomycorrhizal Fungi of Coccoloba uvifera

The /tomentella-thelephora lineage is one of the most highly dominant clades among ectomycorrhizal communities worldwide. Despite its importance as a root symbiont, its fruit bodies are inconspicuous and rarely found. Knowledge regarding the diversity of Tomentella in the Neotropics is scarce, and is based largely on environmental samples. Here, we describe a new species, Tomentella brunneoincrustata, including its basidiocarp morphology, mycorrhizal anatomy, and ecology. Because knowledge of Tomentella in Mexico is scarce, we provide the first phylogenetic analysis of this genus in the country. We sequenced the nrITS region of the fungal samples, and sequenced the rbcL and trnL regions to identify the host plant. The phylogenetic analyses were conducted by Bayesian inference. The Bayesian analysis showed that several paraphyletic clades within the lineage /tomentella-thelephora are associated with Pisonieae present across tropical regions of the world. However, the ectomycorrhizae sequences from Puerto Rico, Florida, Dominica, and Mexico constituted a well-supported monophyletic clade that we denote as the “Pisonieae-associated Neotropical Tomentella clade”. Within this clade, T. brunneoincrustata was characterized as follows: a thin crustose, strongly attached to the substrate basidiome; concolorous subiculum, undifferentiated and sterile margin; two types of subiculum hyphae; and small (<8 μm) globose to ellipsoid spores. This species develops in tropical dry forests, where it associates with hosts in the Pisonieae tribe within the Nyctaginaceae. The remaining Tomentella fruit body vouchers collected in temperate forests of Mexico belonged to clades related to T. atramentaria, T. pilosa, T. muricata, T. fuscocinerea, T. stuposa, T. punicea, T. atroarenicolor, T. bryophila, and T. lateritia. Five fruit body vouchers had unique sequences forming independent and unknown clades of Tomentella.

Tomentella brunneoincrustata, the first described species of the Pisonieae-associated Neotropical Tomentella clade, and phylogenetic analysis of the genus in Mexico

Taxonomy and phylogeny of Hydnellum gracilipes (P. Karst.) P. Karst. (Thelephorales, Hymenomycetes) was revised. The species is characterized by soft and resupinate sporocarps, and the morphology supports a close relationship with tomentelloid fungi. The phylogenetic interpretation of the sequence data from the 5' end of nuclear large subunit (nucLSU) rDNA showed, however, that the closest relatives of H. gracilipes are found in the genus Hydnellum P. Karst. The evolution of the resupinate fruitbody is outlined. The ecology of the species is discussed and it is proposed that H. gracilipes is a mycorrhizal fungus. Six new localities are listed.

Urmas Kõljalg

Papers

The UNITE Database for Molecular Identification and for Communicating Fungal Species

Studies in African thelephoroid fungi: 1. Tomentella capitata and Tomentella brunneocystidia , two new species from Benin (West Africa) with capitate cystidia

Biogeography and Specificity of Ectomycorrhizal Fungi of Coccoloba uvifera

Tomentella brunneoincrustata, the first described species of the Pisonieae-associated Neotropical Tomentella clade, and phylogenetic analysis of the genus in Mexico

Hydnellum gracilipes: a link between stipitate and resupinate Hymenomycetes